npm - nemar-cli - Versions diffs - 0.7.13-dev.420 → 0.7.13-dev.424 - Mend

nemar-cli 0.7.13-dev.420 → 0.7.13-dev.424

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Files changed (2) hide show

package/dist/index.js +72 -74
package/package.json +1 -1

package/dist/index.js CHANGED Viewed

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this._addCheck({kind:"length",value:D,...u.errToObj(F)})}nonempty(D){return this.min(1,u.errToObj(D))}trim(){return new g1({...this._def,checks:[...this._def.checks,{kind:"trim"}]})}toLowerCase(){return new g1({...this._def,checks:[...this._def.checks,{kind:"toLowerCase"}]})}toUpperCase(){return new g1({...this._def,checks:[...this._def.checks,{kind:"toUpperCase"}]})}get isDatetime(){return!!this._def.checks.find((D)=>D.kind==="datetime")}get isDate(){return!!this._def.checks.find((D)=>D.kind==="date")}get isTime(){return!!this._def.checks.find((D)=>D.kind==="time")}get isDuration(){return!!this._def.checks.find((D)=>D.kind==="duration")}get isEmail(){return!!this._def.checks.find((D)=>D.kind==="email")}get isURL(){return!!this._def.checks.find((D)=>D.kind==="url")}get isEmoji(){return!!this._def.checks.find((D)=>D.kind==="emoji")}get isUUID(){return!!this._def.checks.find((D)=>D.kind==="uuid")}get isNANOID(){return!!this._def.checks.find((D)=>D.kind==="nanoid")}get isCUID(){return!!this._def.checks.find((D)=>D.kind==="cuid")}get isCUID2(){return!!this._def.checks.find((D)=>D.kind==="cuid2")}get isULID(){return!!this._def.checks.find((D)=>D.kind==="ulid")}get isIP(){return!!this._def.checks.find((D)=>D.kind==="ip")}get isCIDR(){return!!this._def.checks.find((D)=>D.kind==="cidr")}get isBase64(){return!!this._def.checks.find((D)=>D.kind==="base64")}get isBase64url(){return!!this._def.checks.find((D)=>D.kind==="base64url")}get minLength(){let D=null;for(let F of this._def.checks)if(F.kind==="min"){if(D===null||F.value>D)D=F.value}return D}get maxLength(){let D=null;for(let F of this._def.checks)if(F.kind==="max"){if(D===null||F.value<D)D=F.value}return D}};g1.create=(D)=>{return new g1({checks:[],typeName:o.ZodString,coerce:D?.coerce??!1,...Y0(D)})};y6=class y6 extends H0{constructor(){super(...arguments);this.min=this.gte,this.max=this.lte,this.step=this.multipleOf}_parse(D){if(this._def.coerce)D.data=Number(D.data);if(this._getType(D)!==S.number){let Q=this._getOrReturnCtx(D);return k(Q,{code:j.invalid_type,expected:S.number,received:Q.parsedType}),c}let $=void 0,J=new ND;for(let Q of this._def.checks)if(Q.kind==="int"){if(!V0.isInteger(D.data))$=this._getOrReturnCtx(D,$),k($,{code:j.invalid_type,expected:"integer",received:"float",message:Q.message}),J.dirty()}else if(Q.kind==="min"){if(Q.inclusive?D.data<Q.value:D.data<=Q.value)$=this._getOrReturnCtx(D,$),k($,{code:j.too_small,minimum:Q.value,type:"number",inclusive:Q.inclusive,exact:!1,message:Q.message}),J.dirty()}else if(Q.kind==="max"){if(Q.inclusive?D.data>Q.value:D.data>=Q.value)$=this._getOrReturnCtx(D,$),k($,{code:j.too_big,maximum:Q.value,type:"number",inclusive:Q.inclusive,exact:!1,message:Q.message}),J.dirty()}else if(Q.kind==="multipleOf"){if(Uq0(D.data,Q.value)!==0)$=this._getOrReturnCtx(D,$),k($,{code:j.not_multiple_of,multipleOf:Q.value,message:Q.message}),J.dirty()}else if(Q.kind==="finite"){if(!Number.isFinite(D.data))$=this._getOrReturnCtx(D,$),k($,{code:j.not_finite,message:Q.message}),J.dirty()}else V0.assertNever(Q);return{status:J.value,value:D.data}}gte(D,F){return this.setLimit("min",D,!0,u.toString(F))}gt(D,F){return this.setLimit("min",D,!1,u.toString(F))}lte(D,F){return this.setLimit("max",D,!0,u.toString(F))}lt(D,F){return this.setLimit("max",D,!1,u.toString(F))}setLimit(D,F,$,J){return new y6({...this._def,checks:[...this._def.checks,{kind:D,value:F,inclusive:$,message:u.toString(J)}]})}_addCheck(D){return new y6({...this._def,checks:[...this._def.checks,D]})}int(D){return this._addCheck({kind:"int",message:u.toString(D)})}positive(D){return this._addCheck({kind:"min",value:0,inclusive:!1,message:u.toString(D)})}negative(D){return this._addCheck({kind:"max",value:0,inclusive:!1,message:u.toString(D)})}nonpositive(D){return this._addCheck({kind:"max",value:0,inclusive:!0,message:u.toString(D)})}nonnegative(D){return this._addCheck({kind:"min",value:0,inclusive:!0,message:u.toString(D)})}multipleOf(D,F){return this._addCheck({kind:"multipleOf",value:D,message:u.toString(F)})}finite(D){return this._addCheck({kind:"finite",message:u.toString(D)})}safe(D){return this._addCheck({kind:"min",inclusive:!0,value:Number.MIN_SAFE_INTEGER,message:u.toString(D)})._addCheck({kind:"max",inclusive:!0,value:Number.MAX_SAFE_INTEGER,message:u.toString(D)})}get minValue(){let D=null;for(let F of this._def.checks)if(F.kind==="min"){if(D===null||F.value>D)D=F.value}return D}get maxValue(){let D=null;for(let F of this._def.checks)if(F.kind==="max"){if(D===null||F.value<D)D=F.value}return D}get isInt(){return!!this._def.checks.find((D)=>D.kind==="int"||D.kind==="multipleOf"&&V0.isInteger(D.value))}get isFinite(){let D=null,F=null;for(let $ of this._def.checks)if($.kind==="finite"||$.kind==="int"||$.kind==="multipleOf")return!0;else if($.kind==="min"){if(F===null||$.value>F)F=$.value}else if($.kind==="max"){if(D===null||$.value<D)D=$.value}return Number.isFinite(F)&&Number.isFinite(D)}};y6.create=(D)=>{return new y6({checks:[],typeName:o.ZodNumber,coerce:D?.coerce||!1,...Y0(D)})};x6=class x6 extends H0{constructor(){super(...arguments);this.min=this.gte,this.max=this.lte}_parse(D){if(this._def.coerce)try{D.data=BigInt(D.data)}catch{return this._getInvalidInput(D)}if(this._getType(D)!==S.bigint)return this._getInvalidInput(D);let $=void 0,J=new ND;for(let Q of this._def.checks)if(Q.kind==="min"){if(Q.inclusive?D.data<Q.value:D.data<=Q.value)$=this._getOrReturnCtx(D,$),k($,{code:j.too_small,type:"bigint",minimum:Q.value,inclusive:Q.inclusive,message:Q.message}),J.dirty()}else if(Q.kind==="max"){if(Q.inclusive?D.data>Q.value:D.data>=Q.value)$=this._getOrReturnCtx(D,$),k($,{code:j.too_big,type:"bigint",maximum:Q.value,inclusive:Q.inclusive,message:Q.message}),J.dirty()}else if(Q.kind==="multipleOf"){if(D.data%Q.value!==BigInt(0))$=this._getOrReturnCtx(D,$),k($,{code:j.not_multiple_of,multipleOf:Q.value,message:Q.message}),J.dirty()}else V0.assertNever(Q);return{status:J.value,value:D.data}}_getInvalidInput(D){let F=this._getOrReturnCtx(D);return k(F,{code:j.invalid_type,expected:S.bigint,received:F.parsedType}),c}gte(D,F){return this.setLimit("min",D,!0,u.toString(F))}gt(D,F){return this.setLimit("min",D,!1,u.toString(F))}lte(D,F){return this.setLimit("max",D,!0,u.toString(F))}lt(D,F){return this.setLimit("max",D,!1,u.toString(F))}setLimit(D,F,$,J){return new x6({...this._def,checks:[...this._def.checks,{kind:D,value:F,inclusive:$,message:u.toString(J)}]})}_addCheck(D){return new x6({...this._def,checks:[...this._def.checks,D]})}positive(D){return this._addCheck({kind:"min",value:BigInt(0),inclusive:!1,message:u.toString(D)})}negative(D){return this._addCheck({kind:"max",value:BigInt(0),inclusive:!1,message:u.toString(D)})}nonpositive(D){return this._addCheck({kind:"max",value:BigInt(0),inclusive:!0,message:u.toString(D)})}nonnegative(D){return this._addCheck({kind:"min",value:BigInt(0),inclusive:!0,message:u.toString(D)})}multipleOf(D,F){return this._addCheck({kind:"multipleOf",value:D,message:u.toString(F)})}get minValue(){let D=null;for(let F of this._def.checks)if(F.kind==="min"){if(D===null||F.value>D)D=F.value}return D}get maxValue(){let D=null;for(let F of this._def.checks)if(F.kind==="max"){if(D===null||F.value<D)D=F.value}return D}};x6.create=(D)=>{return new x6({checks:[],typeName:o.ZodBigInt,coerce:D?.coerce??!1,...Y0(D)})};FF=class FF extends H0{_parse(D){if(this._def.coerce)D.data=Boolean(D.data);if(this._getType(D)!==S.boolean){let $=this._getOrReturnCtx(D);return k($,{code:j.invalid_type,expected:S.boolean,received:$.parsedType}),c}return jD(D.data)}};FF.create=(D)=>{return new FF({typeName:o.ZodBoolean,coerce:D?.coerce||!1,...Y0(D)})};A4=class A4 extends H0{_parse(D){if(this._def.coerce)D.data=new Date(D.data);if(this._getType(D)!==S.date){let Q=this._getOrReturnCtx(D);return k(Q,{code:j.invalid_type,expected:S.date,received:Q.parsedType}),c}if(Number.isNaN(D.data.getTime())){let Q=this._getOrReturnCtx(D);return k(Q,{code:j.invalid_date}),c}let $=new ND,J=void 0;for(let Q of this._def.checks)if(Q.kind==="min"){if(D.data.getTime()<Q.value)J=this._getOrReturnCtx(D,J),k(J,{code:j.too_small,message:Q.message,inclusive:!0,exact:!1,minimum:Q.value,type:"date"}),$.dirty()}else if(Q.kind==="max"){if(D.data.getTime()>Q.value)J=this._getOrReturnCtx(D,J),k(J,{code:j.too_big,message:Q.message,inclusive:!0,exact:!1,maximum:Q.value,type:"date"}),$.dirty()}else V0.assertNever(Q);return{status:$.value,value:new Date(D.data.getTime())}}_addCheck(D){return new A4({...this._def,checks:[...this._def.checks,D]})}min(D,F){return this._addCheck({kind:"min",value:D.getTime(),message:u.toString(F)})}max(D,F){return this._addCheck({kind:"max",value:D.getTime(),message:u.toString(F)})}get minDate(){let D=null;for(let F of this._def.checks)if(F.kind==="min"){if(D===null||F.value>D)D=F.value}return D!=null?new Date(D):null}get maxDate(){let D=null;for(let F of this._def.checks)if(F.kind==="max"){if(D===null||F.value<D)D=F.value}return D!=null?new Date(D):null}};A4.create=(D)=>{return new A4({checks:[],coerce:D?.coerce||!1,typeName:o.ZodDate,...Y0(D)})};G9=class G9 extends H0{_parse(D){if(this._getType(D)!==S.symbol){let $=this._getOrReturnCtx(D);return k($,{code:j.invalid_type,expected:S.symbol,received:$.parsedType}),c}return jD(D.data)}};G9.create=(D)=>{return new G9({typeName:o.ZodSymbol,...Y0(D)})};$F=class $F extends H0{_parse(D){if(this._getType(D)!==S.undefined){let $=this._getOrReturnCtx(D);return k($,{code:j.invalid_type,expected:S.undefined,received:$.parsedType}),c}return jD(D.data)}};$F.create=(D)=>{return new $F({typeName:o.ZodUndefined,...Y0(D)})};JF=class JF extends H0{_parse(D){if(this._getType(D)!==S.null){let $=this._getOrReturnCtx(D);return k($,{code:j.invalid_type,expected:S.null,received:$.parsedType}),c}return jD(D.data)}};JF.create=(D)=>{return new JF({typeName:o.ZodNull,...Y0(D)})};L4=class L4 extends H0{constructor(){super(...arguments);this._any=!0}_parse(D){return jD(D.data)}};L4.create=(D)=>{return new L4({typeName:o.ZodAny,...Y0(D)})};v6=class v6 extends H0{constructor(){super(...arguments);this._unknown=!0}_parse(D){return jD(D.data)}};v6.create=(D)=>{return new v6({typeName:o.ZodUnknown,...Y0(D)})};E8=class E8 extends H0{_parse(D){let F=this._getOrReturnCtx(D);return k(F,{code:j.invalid_type,expected:S.never,received:F.parsedType}),c}};E8.create=(D)=>{return new E8({typeName:o.ZodNever,...Y0(D)})};W9=class W9 extends H0{_parse(D){if(this._getType(D)!==S.undefined){let $=this._getOrReturnCtx(D);return k($,{code:j.invalid_type,expected:S.void,received:$.parsedType}),c}return jD(D.data)}};W9.create=(D)=>{return new W9({typeName:o.ZodVoid,...Y0(D)})};h1=class h1 extends H0{_parse(D){let{ctx:F,status:$}=this._processInputParams(D),J=this._def;if(F.parsedType!==S.array)return k(F,{code:j.invalid_type,expected:S.array,received:F.parsedType}),c;if(J.exactLength!==null){let B=F.data.length>J.exactLength.value,Y=F.data.length<J.exactLength.value;if(B||Y)k(F,{code:B?j.too_big:j.too_small,minimum:Y?J.exactLength.value:void 0,maximum:B?J.exactLength.value:void 0,type:"array",inclusive:!0,exact:!0,message:J.exactLength.message}),$.dirty()}if(J.minLength!==null){if(F.data.length<J.minLength.value)k(F,{code:j.too_small,minimum:J.minLength.value,type:"array",inclusive:!0,exact:!1,message:J.minLength.message}),$.dirty()}if(J.maxLength!==null){if(F.data.length>J.maxLength.value)k(F,{code:j.too_big,maximum:J.maxLength.value,type:"array",inclusive:!0,exact:!1,message:J.maxLength.message}),$.dirty()}if(F.common.async)return Promise.all([...F.data].map((B,Y)=>{return J.type._parseAsync(new u1(F,B,F.path,Y))})).then((B)=>{return ND.mergeArray($,B)});let Q=[...F.data].map((B,Y)=>{return J.type._parseSync(new u1(F,B,F.path,Y))});return ND.mergeArray($,Q)}get element(){return this._def.type}min(D,F){return new h1({...this._def,minLength:{value:D,message:u.toString(F)}})}max(D,F){return new h1({...this._def,maxLength:{value:D,message:u.toString(F)}})}length(D,F){return new h1({...this._def,exactLength:{value:D,message:u.toString(F)}})}nonempty(D){return this.min(1,D)}};h1.create=(D,F)=>{return new h1({type:D,minLength:null,maxLength:null,exactLength:null,typeName:o.ZodArray,...Y0(F)})};i0=class i0 extends H0{constructor(){super(...arguments);this._cached=null,this.nonstrict=this.passthrough,this.augment=this.extend}_getCached(){if(this._cached!==null)return this._cached;let D=this._def.shape(),F=V0.objectKeys(D);return this._cached={shape:D,keys:F},this._cached}_parse(D){if(this._getType(D)!==S.object){let G=this._getOrReturnCtx(D);return k(G,{code:j.invalid_type,expected:S.object,received:G.parsedType}),c}let{status:$,ctx:J}=this._processInputParams(D),{shape:Q,keys:B}=this._getCached(),Y=[];if(!(this._def.catchall instanceof E8&&this._def.unknownKeys==="strip")){for(let G in J.data)if(!B.includes(G))Y.push(G)}let X=[];for(let G of B){let W=Q[G],q=J.data[G];X.push({key:{status:"valid",value:G},value:W._parse(new u1(J,q,J.path,G)),alwaysSet:G in J.data})}if(this._def.catchall instanceof E8){let G=this._def.unknownKeys;if(G==="passthrough")for(let W of Y)X.push({key:{status:"valid",value:W},value:{status:"valid",value:J.data[W]}});else if(G==="strict"){if(Y.length>0)k(J,{code:j.unrecognized_keys,keys:Y}),$.dirty()}else if(G==="strip");else throw Error("Internal ZodObject error: invalid unknownKeys value.")}else{let G=this._def.catchall;for(let W of Y){let q=J.data[W];X.push({key:{status:"valid",value:W},value:G._parse(new u1(J,q,J.path,W)),alwaysSet:W in J.data})}}if(J.common.async)return Promise.resolve().then(async()=>{let G=[];for(let W of X){let q=await W.key,K=await W.value;G.push({key:q,value:K,alwaysSet:W.alwaysSet})}return G}).then((G)=>{return ND.mergeObjectSync($,G)});else return ND.mergeObjectSync($,X)}get shape(){return this._def.shape()}strict(D){return u.errToObj,new i0({...this._def,unknownKeys:"strict",...D!==void 0?{errorMap:(F,$)=>{let J=this._def.errorMap?.(F,$).message??$.defaultError;if(F.code==="unrecognized_keys")return{message:u.errToObj(D).message??J};return{message:J}}}:{}})}strip(){return new i0({...this._def,unknownKeys:"strip"})}passthrough(){return new i0({...this._def,unknownKeys:"passthrough"})}extend(D){return new i0({...this._def,shape:()=>({...this._def.shape(),...D})})}merge(D){return new i0({unknownKeys:D._def.unknownKeys,catchall:D._def.catchall,shape:()=>({...this._def.shape(),...D._def.shape()}),typeName:o.ZodObject})}setKey(D,F){return this.augment({[D]:F})}catchall(D){return new i0({...this._def,catchall:D})}pick(D){let F={};for(let $ of V0.objectKeys(D))if(D[$]&&this.shape[$])F[$]=this.shape[$];return new i0({...this._def,shape:()=>F})}omit(D){let F={};for(let $ of V0.objectKeys(this.shape))if(!D[$])F[$]=this.shape[$];return new i0({...this._def,shape:()=>F})}deepPartial(){return e3(this)}partial(D){let F={};for(let $ of V0.objectKeys(this.shape)){let J=this.shape[$];if(D&&!D[$])F[$]=J;else F[$]=J.optional()}return new i0({...this._def,shape:()=>F})}required(D){let F={};for(let $ of V0.objectKeys(this.shape))if(D&&!D[$])F[$]=this.shape[$];else{let Q=this.shape[$];while(Q instanceof b1)Q=Q._def.innerType;F[$]=Q}return new i0({...this._def,shape:()=>F})}keyof(){return ox(V0.objectKeys(this.shape))}};i0.create=(D,F)=>{return new i0({shape:()=>D,unknownKeys:"strip",catchall:E8.create(),typeName:o.ZodObject,...Y0(F)})};i0.strictCreate=(D,F)=>{return new i0({shape:()=>D,unknownKeys:"strict",catchall:E8.create(),typeName:o.ZodObject,...Y0(F)})};i0.lazycreate=(D,F)=>{return new i0({shape:D,unknownKeys:"strip",catchall:E8.create(),typeName:o.ZodObject,...Y0(F)})};QF=class QF extends H0{_parse(D){let{ctx:F}=this._processInputParams(D),$=this._def.options;function J(Q){for(let Y of Q)if(Y.result.status==="valid")return Y.result;for(let Y of Q)if(Y.result.status==="dirty")return F.common.issues.push(...Y.ctx.common.issues),Y.result;let B=Q.map((Y)=>new dD(Y.ctx.common.issues));return k(F,{code:j.invalid_union,unionErrors:B}),c}if(F.common.async)return Promise.all($.map(async(Q)=>{let B={...F,common:{...F.common,issues:[]},parent:null};return{result:await Q._parseAsync({data:F.data,path:F.path,parent:B}),ctx:B}})).then(J);else{let Q=void 0,B=[];for(let X of $){let G={...F,common:{...F.common,issues:[]},parent:null},W=X._parseSync({data:F.data,path:F.path,parent:G});if(W.status==="valid")return W;else if(W.status==="dirty"&&!Q)Q={result:W,ctx:G};if(G.common.issues.length)B.push(G.common.issues)}if(Q)return F.common.issues.push(...Q.ctx.common.issues),Q.result;let Y=B.map((X)=>new dD(X));return k(F,{code:j.invalid_union,unionErrors:Y}),c}}get options(){return this._def.options}};QF.create=(D,F)=>{return new QF({options:D,typeName:o.ZodUnion,...Y0(F)})};IJ=class IJ extends H0{_parse(D){let{ctx:F}=this._processInputParams(D);if(F.parsedType!==S.object)return k(F,{code:j.invalid_type,expected:S.object,received:F.parsedType}),c;let $=this.discriminator,J=F.data[$],Q=this.optionsMap.get(J);if(!Q)return k(F,{code:j.invalid_union_discriminator,options:Array.from(this.optionsMap.keys()),path:[$]}),c;if(F.common.async)return Q._parseAsync({data:F.data,path:F.path,parent:F});else return Q._parseSync({data:F.data,path:F.path,parent:F})}get discriminator(){return this._def.discriminator}get options(){return this._def.options}get optionsMap(){return this._def.optionsMap}static create(D,F,$){let J=new Map;for(let Q of F){let B=u8(Q.shape[D]);if(!B.length)throw Error(`A discriminator value for key \`${D}\` could not be extracted from all schema options`);for(let Y of B){if(J.has(Y))throw Error(`Discriminator property ${String(D)} has duplicate value ${String(Y)}`);J.set(Y,Q)}}return new IJ({typeName:o.ZodDiscriminatedUnion,discriminator:D,options:F,optionsMap:J,...Y0($)})}};BF=class BF extends H0{_parse(D){let{status:F,ctx:$}=this._processInputParams(D),J=(Q,B)=>{if(jJ(Q)||jJ(B))return c;let 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this._addCheck({kind:"min",value:BigInt(0),inclusive:!1,message:u.toString(D)})}negative(D){return this._addCheck({kind:"max",value:BigInt(0),inclusive:!1,message:u.toString(D)})}nonpositive(D){return this._addCheck({kind:"max",value:BigInt(0),inclusive:!0,message:u.toString(D)})}nonnegative(D){return this._addCheck({kind:"min",value:BigInt(0),inclusive:!0,message:u.toString(D)})}multipleOf(D,F){return this._addCheck({kind:"multipleOf",value:D,message:u.toString(F)})}get minValue(){let D=null;for(let F of this._def.checks)if(F.kind==="min"){if(D===null||F.value>D)D=F.value}return D}get maxValue(){let D=null;for(let F of this._def.checks)if(F.kind==="max"){if(D===null||F.value<D)D=F.value}return D}};x6.create=(D)=>{return new x6({checks:[],typeName:o.ZodBigInt,coerce:D?.coerce??!1,...Y0(D)})};FF=class FF extends H0{_parse(D){if(this._def.coerce)D.data=Boolean(D.data);if(this._getType(D)!==S.boolean){let $=this._getOrReturnCtx(D);return 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A4({...this._def,checks:[...this._def.checks,D]})}min(D,F){return this._addCheck({kind:"min",value:D.getTime(),message:u.toString(F)})}max(D,F){return this._addCheck({kind:"max",value:D.getTime(),message:u.toString(F)})}get minDate(){let D=null;for(let F of this._def.checks)if(F.kind==="min"){if(D===null||F.value>D)D=F.value}return D!=null?new Date(D):null}get maxDate(){let D=null;for(let F of this._def.checks)if(F.kind==="max"){if(D===null||F.value<D)D=F.value}return D!=null?new Date(D):null}};A4.create=(D)=>{return new A4({checks:[],coerce:D?.coerce||!1,typeName:o.ZodDate,...Y0(D)})};G9=class G9 extends H0{_parse(D){if(this._getType(D)!==S.symbol){let $=this._getOrReturnCtx(D);return k($,{code:j.invalid_type,expected:S.symbol,received:$.parsedType}),c}return jD(D.data)}};G9.create=(D)=>{return new G9({typeName:o.ZodSymbol,...Y0(D)})};$F=class $F extends H0{_parse(D){if(this._getType(D)!==S.undefined){let $=this._getOrReturnCtx(D);return k($,{code:j.invalid_type,expected:S.undefined,received:$.parsedType}),c}return jD(D.data)}};$F.create=(D)=>{return new $F({typeName:o.ZodUndefined,...Y0(D)})};JF=class JF extends H0{_parse(D){if(this._getType(D)!==S.null){let $=this._getOrReturnCtx(D);return k($,{code:j.invalid_type,expected:S.null,received:$.parsedType}),c}return jD(D.data)}};JF.create=(D)=>{return new JF({typeName:o.ZodNull,...Y0(D)})};L4=class L4 extends H0{constructor(){super(...arguments);this._any=!0}_parse(D){return jD(D.data)}};L4.create=(D)=>{return new L4({typeName:o.ZodAny,...Y0(D)})};v6=class v6 extends H0{constructor(){super(...arguments);this._unknown=!0}_parse(D){return jD(D.data)}};v6.create=(D)=>{return new v6({typeName:o.ZodUnknown,...Y0(D)})};E8=class E8 extends H0{_parse(D){let F=this._getOrReturnCtx(D);return k(F,{code:j.invalid_type,expected:S.never,received:F.parsedType}),c}};E8.create=(D)=>{return new E8({typeName:o.ZodNever,...Y0(D)})};W9=class W9 extends H0{_parse(D){if(this._getType(D)!==S.undefined){let $=this._getOrReturnCtx(D);return k($,{code:j.invalid_type,expected:S.void,received:$.parsedType}),c}return jD(D.data)}};W9.create=(D)=>{return new W9({typeName:o.ZodVoid,...Y0(D)})};h1=class h1 extends H0{_parse(D){let{ctx:F,status:$}=this._processInputParams(D),J=this._def;if(F.parsedType!==S.array)return k(F,{code:j.invalid_type,expected:S.array,received:F.parsedType}),c;if(J.exactLength!==null){let B=F.data.length>J.exactLength.value,Y=F.data.length<J.exactLength.value;if(B||Y)k(F,{code:B?j.too_big:j.too_small,minimum:Y?J.exactLength.value:void 0,maximum:B?J.exactLength.value:void 0,type:"array",inclusive:!0,exact:!0,message:J.exactLength.message}),$.dirty()}if(J.minLength!==null){if(F.data.length<J.minLength.value)k(F,{code:j.too_small,minimum:J.minLength.value,type:"array",inclusive:!0,exact:!1,message:J.minLength.message}),$.dirty()}if(J.maxLength!==null){if(F.data.length>J.maxLength.value)k(F,{code:j.too_big,maximum:J.maxLength.value,type:"array",inclusive:!0,exact:!1,message:J.maxLength.message}),$.dirty()}if(F.common.async)return Promise.all([...F.data].map((B,Y)=>{return J.type._parseAsync(new u1(F,B,F.path,Y))})).then((B)=>{return ND.mergeArray($,B)});let Q=[...F.data].map((B,Y)=>{return J.type._parseSync(new u1(F,B,F.path,Y))});return ND.mergeArray($,Q)}get element(){return this._def.type}min(D,F){return new h1({...this._def,minLength:{value:D,message:u.toString(F)}})}max(D,F){return new h1({...this._def,maxLength:{value:D,message:u.toString(F)}})}length(D,F){return new h1({...this._def,exactLength:{value:D,message:u.toString(F)}})}nonempty(D){return this.min(1,D)}};h1.create=(D,F)=>{return new h1({type:D,minLength:null,maxLength:null,exactLength:null,typeName:o.ZodArray,...Y0(F)})};i0=class i0 extends H0{constructor(){super(...arguments);this._cached=null,this.nonstrict=this.passthrough,this.augment=this.extend}_getCached(){if(this._cached!==null)return this._cached;let D=this._def.shape(),F=V0.objectKeys(D);return this._cached={shape:D,keys:F},this._cached}_parse(D){if(this._getType(D)!==S.object){let G=this._getOrReturnCtx(D);return k(G,{code:j.invalid_type,expected:S.object,received:G.parsedType}),c}let{status:$,ctx:J}=this._processInputParams(D),{shape:Q,keys:B}=this._getCached(),Y=[];if(!(this._def.catchall instanceof E8&&this._def.unknownKeys==="strip")){for(let G in J.data)if(!B.includes(G))Y.push(G)}let X=[];for(let G of B){let W=Q[G],q=J.data[G];X.push({key:{status:"valid",value:G},value:W._parse(new u1(J,q,J.path,G)),alwaysSet:G in J.data})}if(this._def.catchall instanceof E8){let G=this._def.unknownKeys;if(G==="passthrough")for(let W of Y)X.push({key:{status:"valid",value:W},value:{status:"valid",value:J.data[W]}});else if(G==="strict"){if(Y.length>0)k(J,{code:j.unrecognized_keys,keys:Y}),$.dirty()}else if(G==="strip");else throw Error("Internal ZodObject error: invalid unknownKeys value.")}else{let G=this._def.catchall;for(let W of Y){let q=J.data[W];X.push({key:{status:"valid",value:W},value:G._parse(new u1(J,q,J.path,W)),alwaysSet:W in J.data})}}if(J.common.async)return Promise.resolve().then(async()=>{let G=[];for(let W of X){let q=await W.key,K=await W.value;G.push({key:q,value:K,alwaysSet:W.alwaysSet})}return G}).then((G)=>{return ND.mergeObjectSync($,G)});else return ND.mergeObjectSync($,X)}get shape(){return this._def.shape()}strict(D){return u.errToObj,new i0({...this._def,unknownKeys:"strict",...D!==void 0?{errorMap:(F,$)=>{let J=this._def.errorMap?.(F,$).message??$.defaultError;if(F.code==="unrecognized_keys")return{message:u.errToObj(D).message??J};return{message:J}}}:{}})}strip(){return new i0({...this._def,unknownKeys:"strip"})}passthrough(){return new i0({...this._def,unknownKeys:"passthrough"})}extend(D){return new i0({...this._def,shape:()=>({...this._def.shape(),...D})})}merge(D){return new i0({unknownKeys:D._def.unknownKeys,catchall:D._def.catchall,shape:()=>({...this._def.shape(),...D._def.shape()}),typeName:o.ZodObject})}setKey(D,F){return this.augment({[D]:F})}catchall(D){return new i0({...this._def,catchall:D})}pick(D){let F={};for(let $ of V0.objectKeys(D))if(D[$]&&this.shape[$])F[$]=this.shape[$];return new i0({...this._def,shape:()=>F})}omit(D){let F={};for(let $ of V0.objectKeys(this.shape))if(!D[$])F[$]=this.shape[$];return new i0({...this._def,shape:()=>F})}deepPartial(){return e3(this)}partial(D){let F={};for(let $ of V0.objectKeys(this.shape)){let J=this.shape[$];if(D&&!D[$])F[$]=J;else F[$]=J.optional()}return new i0({...this._def,shape:()=>F})}required(D){let F={};for(let $ of V0.objectKeys(this.shape))if(D&&!D[$])F[$]=this.shape[$];else{let Q=this.shape[$];while(Q instanceof b1)Q=Q._def.innerType;F[$]=Q}return new i0({...this._def,shape:()=>F})}keyof(){return ox(V0.objectKeys(this.shape))}};i0.create=(D,F)=>{return new i0({shape:()=>D,unknownKeys:"strip",catchall:E8.create(),typeName:o.ZodObject,...Y0(F)})};i0.strictCreate=(D,F)=>{return new i0({shape:()=>D,unknownKeys:"strict",catchall:E8.create(),typeName:o.ZodObject,...Y0(F)})};i0.lazycreate=(D,F)=>{return new i0({shape:D,unknownKeys:"strip",catchall:E8.create(),typeName:o.ZodObject,...Y0(F)})};QF=class QF extends H0{_parse(D){let{ctx:F}=this._processInputParams(D),$=this._def.options;function J(Q){for(let Y of Q)if(Y.result.status==="valid")return Y.result;for(let Y of Q)if(Y.result.status==="dirty")return F.common.issues.push(...Y.ctx.common.issues),Y.result;let B=Q.map((Y)=>new dD(Y.ctx.common.issues));return k(F,{code:j.invalid_union,unionErrors:B}),c}if(F.common.async)return Promise.all($.map(async(Q)=>{let B={...F,common:{...F.common,issues:[]},parent:null};return{result:await Q._parseAsync({data:F.data,path:F.path,parent:B}),ctx:B}})).then(J);else{let Q=void 0,B=[];for(let X of $){let G={...F,common:{...F.common,issues:[]},parent:null},W=X._parseSync({data:F.data,path:F.path,parent:G});if(W.status==="valid")return W;else if(W.status==="dirty"&&!Q)Q={result:W,ctx:G};if(G.common.issues.length)B.push(G.common.issues)}if(Q)return F.common.issues.push(...Q.ctx.common.issues),Q.result;let Y=B.map((X)=>new dD(X));return k(F,{code:j.invalid_union,unionErrors:Y}),c}}get options(){return this._def.options}};QF.create=(D,F)=>{return new QF({options:D,typeName:o.ZodUnion,...Y0(F)})};IJ=class IJ extends H0{_parse(D){let{ctx:F}=this._processInputParams(D);if(F.parsedType!==S.object)return k(F,{code:j.invalid_type,expected:S.object,received:F.parsedType}),c;let $=this.discriminator,J=F.data[$],Q=this.optionsMap.get(J);if(!Q)return k(F,{code:j.invalid_union_discriminator,options:Array.from(this.optionsMap.keys()),path:[$]}),c;if(F.common.async)return Q._parseAsync({data:F.data,path:F.path,parent:F});else return Q._parseSync({data:F.data,path:F.path,parent:F})}get discriminator(){return this._def.discriminator}get options(){return this._def.options}get optionsMap(){return this._def.optionsMap}static create(D,F,$){let J=new Map;for(let Q of F){let B=u8(Q.shape[D]);if(!B.length)throw Error(`A discriminator value for key \`${D}\` could not be extracted from all schema options`);for(let Y of B){if(J.has(Y))throw Error(`Discriminator property ${String(D)} has duplicate value ${String(Y)}`);J.set(Y,Q)}}return new IJ({typeName:o.ZodDiscriminatedUnion,discriminator:D,options:F,optionsMap:J,...Y0($)})}};BF=class BF extends H0{_parse(D){let{status:F,ctx:$}=this._processInputParams(D),J=(Q,B)=>{if(jJ(Q)||jJ(B))return c;let Y=aG(Q.value,B.value);if(!Y.valid)return k($,{code:j.invalid_intersection_types}),c;if(PJ(Q)||PJ(B))F.dirty();return{status:F.value,value:Y.data}};if($.common.async)return Promise.all([this._def.left._parseAsync({data:$.data,path:$.path,parent:$}),this._def.right._parseAsync({data:$.data,path:$.path,parent:$})]).then(([Q,B])=>J(Q,B));else return J(this._def.left._parseSync({data:$.data,path:$.path,parent:$}),this._def.right._parseSync({data:$.data,path:$.path,parent:$}))}};BF.create=(D,F,$)=>{return new BF({left:D,right:F,typeName:o.ZodIntersection,...Y0($)})};z8=class z8 extends H0{_parse(D){let{status:F,ctx:$}=this._processInputParams(D);if($.parsedType!==S.array)return k($,{code:j.invalid_type,expected:S.array,received:$.parsedType}),c;if($.data.length<this._def.items.length)return k($,{code:j.too_small,minimum:this._def.items.length,inclusive:!0,exact:!1,type:"array"}),c;if(!this._def.rest&&$.data.length>this._def.items.length)k($,{code:j.too_big,maximum:this._def.items.length,inclusive:!0,exact:!1,type:"array"}),F.dirty();let Q=[...$.data].map((B,Y)=>{let X=this._def.items[Y]||this._def.rest;if(!X)return null;return X._parse(new u1($,B,$.path,Y))}).filter((B)=>!!B);if($.common.async)return Promise.all(Q).then((B)=>{return ND.mergeArray(F,B)});else return ND.mergeArray(F,Q)}get items(){return this._def.items}rest(D){return new z8({...this._def,rest:D})}};z8.create=(D,F)=>{if(!Array.isArray(D))throw Error("You must pass an array of schemas to z.tuple([ ... ])");return new z8({items:D,typeName:o.ZodTuple,rest:null,...Y0(F)})};H9=class H9 extends H0{get keySchema(){return this._def.keyType}get valueSchema(){return this._def.valueType}_parse(D){let{status:F,ctx:$}=this._processInputParams(D);if($.parsedType!==S.object)return k($,{code:j.invalid_type,expected:S.object,received:$.parsedType}),c;let J=[],Q=this._def.keyType,B=this._def.valueType;for(let Y in $.data)J.push({key:Q._parse(new u1($,Y,$.path,Y)),value:B._parse(new u1($,$.data[Y],$.path,Y)),alwaysSet:Y in $.data});if($.common.async)return ND.mergeObjectAsync(F,J);else return ND.mergeObjectSync(F,J)}get element(){return this._def.valueType}static create(D,F,$){if(F instanceof H0)return new H9({keyType:D,valueType:F,typeName:o.ZodRecord,...Y0($)});return new H9({keyType:g1.create(),valueType:D,typeName:o.ZodRecord,...Y0(F)})}};q9=class q9 extends H0{get keySchema(){return this._def.keyType}get valueSchema(){return this._def.valueType}_parse(D){let{status:F,ctx:$}=this._processInputParams(D);if($.parsedType!==S.map)return k($,{code:j.invalid_type,expected:S.map,received:$.parsedType}),c;let J=this._def.keyType,Q=this._def.valueType,B=[...$.data.entries()].map(([Y,X],G)=>{return{key:J._parse(new u1($,Y,$.path,[G,"key"])),value:Q._parse(new u1($,X,$.path,[G,"value"]))}});if($.common.async){let Y=new Map;return Promise.resolve().then(async()=>{for(let X of B){let G=await X.key,W=await X.value;if(G.status==="aborted"||W.status==="aborted")return c;if(G.status==="dirty"||W.status==="dirty")F.dirty();Y.set(G.value,W.value)}return{status:F.value,value:Y}})}else{let Y=new Map;for(let X of B){let{key:G,value:W}=X;if(G.status==="aborted"||W.status==="aborted")return c;if(G.status==="dirty"||W.status==="dirty")F.dirty();Y.set(G.value,W.value)}return{status:F.value,value:Y}}}};q9.create=(D,F,$)=>{return new q9({valueType:F,keyType:D,typeName:o.ZodMap,...Y0($)})};M4=class M4 extends H0{_parse(D){let{status:F,ctx:$}=this._processInputParams(D);if($.parsedType!==S.set)return k($,{code:j.invalid_type,expected:S.set,received:$.parsedType}),c;let J=this._def;if(J.minSize!==null){if($.data.size<J.minSize.value)k($,{code:j.too_small,minimum:J.minSize.value,type:"set",inclusive:!0,exact:!1,message:J.minSize.message}),F.dirty()}if(J.maxSize!==null){if($.data.size>J.maxSize.value)k($,{code:j.too_big,maximum:J.maxSize.value,type:"set",inclusive:!0,exact:!1,message:J.maxSize.message}),F.dirty()}let Q=this._def.valueType;function B(X){let G=new Set;for(let W of X){if(W.status==="aborted")return c;if(W.status==="dirty")F.dirty();G.add(W.value)}return{status:F.value,value:G}}let Y=[...$.data.values()].map((X,G)=>Q._parse(new u1($,X,$.path,G)));if($.common.async)return Promise.all(Y).then((X)=>B(X));else return B(Y)}min(D,F){return new M4({...this._def,minSize:{value:D,message:u.toString(F)}})}max(D,F){return new M4({...this._def,maxSize:{value:D,message:u.toString(F)}})}size(D,F){return this.min(D,F).max(D,F)}nonempty(D){return this.min(1,D)}};M4.create=(D,F)=>{return new M4({valueType:D,minSize:null,maxSize:null,typeName:o.ZodSet,...Y0(F)})};DF=class DF extends H0{constructor(){super(...arguments);this.validate=this.implement}_parse(D){let{ctx:F}=this._processInputParams(D);if(F.parsedType!==S.function)return k(F,{code:j.invalid_type,expected:S.function,received:F.parsedType}),c;function $(Y,X){return X9({data:Y,path:F.path,errorMaps:[F.common.contextualErrorMap,F.schemaErrorMap,r3(),b8].filter((G)=>!!G),issueData:{code:j.invalid_arguments,argumentsError:X}})}function J(Y,X){return X9({data:Y,path:F.path,errorMaps:[F.common.contextualErrorMap,F.schemaErrorMap,r3(),b8].filter((G)=>!!G),issueData:{code:j.invalid_return_type,returnTypeError:X}})}let Q={errorMap:F.common.contextualErrorMap},B=F.data;if(this._def.returns instanceof N4){let Y=this;return jD(async function(...X){let G=new dD([]),W=await Y._def.args.parseAsync(X,Q).catch((Z)=>{throw G.addIssue($(X,Z)),G}),q=await Reflect.apply(B,this,W);return await Y._def.returns._def.type.parseAsync(q,Q).catch((Z)=>{throw G.addIssue(J(q,Z)),G})})}else{let Y=this;return jD(function(...X){let G=Y._def.args.safeParse(X,Q);if(!G.success)throw new dD([$(X,G.error)]);let W=Reflect.apply(B,this,G.data),q=Y._def.returns.safeParse(W,Q);if(!q.success)throw new dD([J(W,q.error)]);return q.data})}}parameters(){return this._def.args}returnType(){return this._def.returns}args(...D){return new DF({...this._def,args:z8.create(D).rest(v6.create())})}returns(D){return new DF({...this._def,returns:D})}implement(D){return this.parse(D)}strictImplement(D){return this.parse(D)}static create(D,F,$){return new DF({args:D?D:z8.create([]).rest(v6.create()),returns:F||v6.create(),typeName:o.ZodFunction,...Y0($)})}};YF=class YF extends H0{get schema(){return this._def.getter()}_parse(D){let{ctx:F}=this._processInputParams(D);return this._def.getter()._parse({data:F.data,path:F.path,parent:F})}};YF.create=(D,F)=>{return new 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   $ nemar admin ci check nm000104          # Check CI status
   $ nemar admin s3 regenerate-iam john_doe # Regenerate AWS credentials
-  $ nemar admin doi create nm000104        # Create concept DOI`);function d0(){if(!v0())return console.log(H.red("Error: Not authenticated")),console.log(H.gray("  Run 'nemar auth login' first")),!1;return!0}KD.command("users").description("List NEMAR users").option("--pending","Show only pending approval").option("--verified","Show only verified (awaiting approval)").option("--approved","Show only approved users").option("--revoked","Show only revoked users").option("--role <role>","Filter by role: owner, admin, or member").addHelpText("after",`
+  $ nemar admin doi create nm000104        # Create concept DOI`);function d0(){if(!v0())return console.log(H.red("Error: Not authenticated")),console.log(H.dim("  Run 'nemar auth login' first")),!1;return!0}KD.command("users").description("List NEMAR users").option("--pending","Show only pending approval").option("--verified","Show only verified (awaiting approval)").option("--approved","Show only approved users").option("--revoked","Show only revoked users").option("--role <role>","Filter by role: owner, admin, or member").addHelpText("after",`
 Examples:
   $ nemar admin users                    # List all users
   $ nemar admin users --verified         # Users awaiting approval
@@ -159,11 +159,11 @@ Examples:
   $ nemar admin users --role owner       # List all owners
   $ nemar admin users --approved --role member  # Approved regular users`).action(async(D)=>{if(!d0())return;let F;if(D.pending)F="pending";else if(D.verified)F="verified";else if(D.approved)F="approved";else if(D.revoked)F="revoked";let $=D.role;if($&&!["owner","admin","member"].includes($))console.error(H.red(`Invalid role '${$}'. Must be: owner, admin, or member`)),process.exit(1);let J=N("Fetching users...").start();try{let Q=await A_(F,$);if(J.stop(),Q.users.length===0){let Y=[F,$].filter(Boolean).join(", ");console.log(H.yellow(`No users found${Y?` (filter: ${Y})`:""}`));return}let B=[F,$?`role=${$}`:""].filter(Boolean).join(", ");console.log(`
 ${H.cyan("NEMAR Users")} (${Q.count} total${B?`, filter: ${B}`:""})
-`);for(let Y of Q.users){let X={pending:H.gray,verified:H.yellow,approved:H.green,revoked:H.red}[Y.status]||H.white,G=Y.role||"member",W=G==="owner"?H.red(" [owner]"):G==="admin"?H.magenta(" [admin]"):H.gray(" [member]"),q=Y.email_verified?"":H.gray(" (unverified)");console.log(`  ${H.cyan(Y.username)}${W}`),console.log(`    Email:   ${Y.email}${q}`),console.log(`    GitHub:  @${Y.github_username}`),console.log(`    Status:  ${X(Y.status)}`),console.log(`    Created: ${new Date(Y.created_at).toLocaleDateString()}`),console.log()}}catch(Q){eD(Q,J,"Failed to fetch users")}});KD.command("approve").description("Approve a pending user").argument("<username>","Username to approve").option(I0,S0).option(a0,g0).action(async(D,F)=>{if(!d0())return;console.log(H.cyan(`
+`);for(let Y of Q.users){let X={pending:H.dim,verified:H.yellow,approved:H.green,revoked:H.red}[Y.status]||H.white,G=Y.role||"member",W=G==="owner"?H.red(" [owner]"):G==="admin"?H.magenta(" [admin]"):H.dim(" [member]"),q=Y.email_verified?"":H.dim(" (unverified)");console.log(`  ${H.cyan(Y.username)}${W}`),console.log(`    Email:   ${Y.email}${q}`),console.log(`    GitHub:  @${Y.github_username}`),console.log(`    Status:  ${X(Y.status)}`),console.log(`    Created: ${new Date(Y.created_at).toLocaleDateString()}`),console.log()}}catch(Q){eD(Q,J,"Failed to fetch users")}});KD.command("approve").description("Approve a pending user").argument("<username>","Username to approve").option(I0,S0).option(a0,g0).action(async(D,F)=>{if(!d0())return;console.log(H.cyan(`
 Approving user: ${D}
-`)),console.log("This will:"),console.log("  1. Set up S3 access for the user"),console.log("  2. Notify them to retrieve their API key via CLI"),console.log();let $=await y0(`Approve ${D}?`,F,!0);if($!=="confirmed"){console.log(H.gray($==="declined"?"Skipped":"Cancelled"));return}let J=N(`Approving ${D}...`).start();try{let Q=await L_(D);if(J.succeed(`Approved ${D}`),console.log(),console.log(`  Email: ${Q.user.email}`),console.log(`  Status: ${H.green(Q.user.status)}`),Q.iam_setup===!0)console.log(`  S3 Access: ${H.green("configured")}`);else if(Q.iam_setup===!1)console.log(`  S3 Access: ${H.red("NOT configured")}`);if(console.log(),Q.email_sent)console.log(H.green("User notified to retrieve their API key via 'nemar auth retrieve-key'"));else console.log(H.yellow("Warning: Notification email failed to send.")),console.log(H.yellow("Please notify the user manually to run 'nemar auth retrieve-key'"));if(Q.warning)console.log(),console.log(H.yellow(`Warning: ${Q.warning}`))}catch(Q){eD(Q,J,"Failed to approve user",{404:"User not found or not in 'verified' status"})}});KD.command("revoke").description("Revoke user access").argument("<username>","Username to revoke").option(I0,S0).option(a0,g0).action(async(D,F)=>{if(!d0())return;if(YD().username===D){console.log(H.red("Error: Cannot revoke your own access"));return}console.log(H.red(`
+`)),console.log("This will:"),console.log("  1. Set up S3 access for the user"),console.log("  2. Notify them to retrieve their API key via CLI"),console.log();let $=await y0(`Approve ${D}?`,F,!0);if($!=="confirmed"){console.log(H.dim($==="declined"?"Skipped":"Cancelled"));return}let J=N(`Approving ${D}...`).start();try{let Q=await L_(D);if(J.succeed(`Approved ${D}`),console.log(),console.log(`  Email: ${Q.user.email}`),console.log(`  Status: ${H.green(Q.user.status)}`),Q.iam_setup===!0)console.log(`  S3 Access: ${H.green("configured")}`);else if(Q.iam_setup===!1)console.log(`  S3 Access: ${H.red("NOT configured")}`);if(console.log(),Q.email_sent)console.log(H.green("User notified to retrieve their API key via 'nemar auth retrieve-key'"));else console.log(H.yellow("Warning: Notification email failed to send.")),console.log(H.yellow("Please notify the user manually to run 'nemar auth retrieve-key'"));if(Q.warning)console.log(),console.log(H.yellow(`Warning: ${Q.warning}`))}catch(Q){eD(Q,J,"Failed to approve user",{404:"User not found or not in 'verified' status"})}});KD.command("revoke").description("Revoke user access").argument("<username>","Username to revoke").option(I0,S0).option(a0,g0).action(async(D,F)=>{if(!d0())return;if(YD().username===D){console.log(H.red("Error: Cannot revoke your own access"));return}console.log(H.red(`
 Revoking access for: ${D}
-`)),console.log(H.yellow("This will:")),console.log("  1. Invalidate all API keys for this user"),console.log("  2. Remove them from datasets they have access to"),console.log("  3. Send them a notification email"),console.log();let J=await s_(`Type '${D}' to confirm revocation:`,D,F);if(J!=="confirmed"){console.log(H.gray(J==="declined"?"Skipped":"Cancelled"));return}let Q=N(`Revoking ${D}...`).start();try{await M_(D),Q.succeed(`Revoked access for ${D}`)}catch(B){eD(B,Q,"Failed to revoke user",{404:"User not found"})}});KD.command("role").description("Change a user's role (owner only)").argument("<username>","Username to change role for").argument("<role>","New role: owner, admin, or member").option("-y, --yes","Skip confirmation prompt").addHelpText("after",`
+`)),console.log(H.yellow("This will:")),console.log("  1. Invalidate all API keys for this user"),console.log("  2. Remove them from datasets they have access to"),console.log("  3. Send them a notification email"),console.log();let J=await s_(`Type '${D}' to confirm revocation:`,D,F);if(J!=="confirmed"){console.log(H.dim(J==="declined"?"Skipped":"Cancelled"));return}let Q=N(`Revoking ${D}...`).start();try{await M_(D),Q.succeed(`Revoked access for ${D}`)}catch(B){eD(B,Q,"Failed to revoke user",{404:"User not found"})}});KD.command("role").description("Change a user's role (owner only)").argument("<username>","Username to change role for").argument("<role>","New role: owner, admin, or member").option("-y, --yes","Skip confirmation prompt").addHelpText("after",`
 Permission Model:
   owner  - Full access: can manage users, roles, datasets, DOIs, and system settings
   admin  - Can approve/revoke users, manage datasets and DOIs
@@ -178,21 +178,21 @@ Rules:
 Examples:
   $ nemar admin role john_doe admin        # Promote to admin
   $ nemar admin role john_doe member       # Demote to member
-  $ nemar admin role jane_doe owner -y     # Promote to owner (skip confirm)`).action(async(D,F,$)=>{if(!d0())return;if(!["owner","admin","member"].includes(F))console.error(H.red(`Invalid role '${F}'. Must be: owner, admin, or member`)),process.exit(1);if(!$.yes){let{confirmed:Q}=await B0.prompt([{type:"confirm",name:"confirmed",message:`Change ${D}'s role to '${F}'?`,default:!1}]);if(!Q){console.log(H.gray("Cancelled"));return}}let J=N(`Changing ${D}'s role to '${F}'...`).start();try{let Q=await N_(D,F);if(J.succeed(Q.message),Q.tokens_revoked!==void 0&&Q.tokens_revoked>0)console.log(H.yellow(`  ${Q.tokens_revoked} token(s) revoked (user must re-login)`))}catch(Q){eD(Q,J,"Failed to change role",{400:"Invalid request (check if you are an owner)",403:"Owner access required",404:"User not found",409:"User already has that role"})}});var XW=new FD("s3").description("S3 and IAM credential management");XW.command("regenerate-iam").description("Regenerate AWS IAM credentials for a user").argument("<username>","Username to regenerate credentials for").option(I0,S0).option(a0,g0).action(yf);XW.command("lock").description("Apply S3 Object Lock (Governance mode) to a dataset").argument("<dataset-id>","Dataset ID to lock").option(I0,S0).option(a0,g0).action(async(D,F)=>{if(!d0())return;console.log(H.cyan(`
+  $ nemar admin role jane_doe owner -y     # Promote to owner (skip confirm)`).action(async(D,F,$)=>{if(!d0())return;if(!["owner","admin","member"].includes(F))console.error(H.red(`Invalid role '${F}'. Must be: owner, admin, or member`)),process.exit(1);if(!$.yes){let{confirmed:Q}=await B0.prompt([{type:"confirm",name:"confirmed",message:`Change ${D}'s role to '${F}'?`,default:!1}]);if(!Q){console.log(H.dim("Cancelled"));return}}let J=N(`Changing ${D}'s role to '${F}'...`).start();try{let Q=await N_(D,F);if(J.succeed(Q.message),Q.tokens_revoked!==void 0&&Q.tokens_revoked>0)console.log(H.yellow(`  ${Q.tokens_revoked} token(s) revoked (user must re-login)`))}catch(Q){eD(Q,J,"Failed to change role",{400:"Invalid request (check if you are an owner)",403:"Owner access required",404:"User not found",409:"User already has that role"})}});var XW=new FD("s3").description("S3 and IAM credential management");XW.command("regenerate-iam").description("Regenerate AWS IAM credentials for a user").argument("<username>","Username to regenerate credentials for").option(I0,S0).option(a0,g0).action(yf);XW.command("lock").description("Apply S3 Object Lock (Governance mode) to a dataset").argument("<dataset-id>","Dataset ID to lock").option(I0,S0).option(a0,g0).action(async(D,F)=>{if(!d0())return;console.log(H.cyan(`
 Apply S3 Object Lock to ${D}
-`)),console.log("This will:"),console.log("  \u2022 Set GOVERNANCE mode Object Lock on all objects"),console.log("  \u2022 Retention period: 100 years"),console.log("  \u2022 Objects cannot be deleted or modified without bypass"),console.log();let $=await y0(`Apply S3 Object Lock to ${D}?`,F);if($!=="confirmed"){console.log(H.gray($==="declined"?"Skipped":"Cancelled"));return}let J=N("Applying S3 Object Lock...").start();try{let Q=await d_(D);if(Q.failed.length>0){J.fail(`Partial lock: ${Q.locked}/${Q.total} locked, ${Q.failed.length} failed`),console.log(H.yellow(`
-Failed objects:`));for(let B of Q.failed.slice(0,10))console.log(`  \u2022 ${B}`);if(Q.failed.length>10)console.log(`  ... and ${Q.failed.length-10} more`)}else J.succeed(`All ${Q.locked} objects locked successfully`)}catch(Q){J.fail("S3 lock failed"),console.log(H.gray(`  ${p0(Q)}`))}});KD.addCommand(XW);KD.command("regenerate-iam",{hidden:!0}).argument("<username>").option(I0,S0).option(a0,g0).action(yf);async function yf(D,F){if(!d0())return;console.log(H.yellow(`
+`)),console.log("This will:"),console.log("  \u2022 Set GOVERNANCE mode Object Lock on all objects"),console.log("  \u2022 Retention period: 100 years"),console.log("  \u2022 Objects cannot be deleted or modified without bypass"),console.log();let $=await y0(`Apply S3 Object Lock to ${D}?`,F);if($!=="confirmed"){console.log(H.dim($==="declined"?"Skipped":"Cancelled"));return}let J=N("Applying S3 Object Lock...").start();try{let Q=await d_(D);if(Q.failed.length>0){J.fail(`Partial lock: ${Q.locked}/${Q.total} locked, ${Q.failed.length} failed`),console.log(H.yellow(`
+Failed objects:`));for(let B of Q.failed.slice(0,10))console.log(`  \u2022 ${B}`);if(Q.failed.length>10)console.log(`  ... and ${Q.failed.length-10} more`)}else J.succeed(`All ${Q.locked} objects locked successfully`)}catch(Q){J.fail("S3 lock failed"),console.log(H.dim(`  ${p0(Q)}`))}});KD.addCommand(XW);KD.command("regenerate-iam",{hidden:!0}).argument("<username>").option(I0,S0).option(a0,g0).action(yf);async function yf(D,F){if(!d0())return;console.log(H.yellow(`
 Regenerate IAM credentials for: ${D}
-`)),console.log("This will:"),console.log("  1. Create new AWS IAM access keys for the user"),console.log("  2. Invalidate any existing access keys"),console.log("  3. Restore S3 access to their datasets"),console.log(),console.log(H.gray("Use this if a user's credentials were compromised or lost.")),console.log();let $=await y0(`Regenerate IAM credentials for ${D}?`,F);if($!=="confirmed"){console.log(H.gray($==="declined"?"Skipped":"Cancelled"));return}let J=N(`Regenerating IAM credentials for ${D}...`).start();try{let Q=await C_(D);if(J.succeed(`Regenerated IAM credentials for ${D}`),console.log(),console.log(`  IAM Username: ${H.cyan(Q.user.iam_username)}`),Q.user.role==="admin"||Q.user.role==="owner")console.log(`  Access: ${H.magenta("full bucket access (admin/owner)")}`);if(console.log(`  Datasets restored: ${H.green(Q.datasets_restored)}`),Q.warning)console.log(),console.log(H.yellow(`  Warning: ${Q.warning}`)),console.log(H.gray("  Please verify old credentials are revoked in AWS console."));console.log(),console.log(H.gray("The user can now upload to their datasets again."))}catch(Q){eD(Q,J,"Failed to regenerate IAM credentials",{404:"User not found or not approved"})}}var GW=new FD("repo").description("Repository visibility management");GW.command("public").description("Make a dataset repository public").argument("<dataset-id>","Dataset ID (e.g., nm000104)").option(I0,S0).option(a0,g0).action(async(D,F)=>{if(!d0())return;console.log(H.cyan(`
+`)),console.log("This will:"),console.log("  1. Create new AWS IAM access keys for the user"),console.log("  2. Invalidate any existing access keys"),console.log("  3. Restore S3 access to their datasets"),console.log(),console.log(H.dim("Use this if a user's credentials were compromised or lost.")),console.log();let $=await y0(`Regenerate IAM credentials for ${D}?`,F);if($!=="confirmed"){console.log(H.dim($==="declined"?"Skipped":"Cancelled"));return}let J=N(`Regenerating IAM credentials for ${D}...`).start();try{let Q=await C_(D);if(J.succeed(`Regenerated IAM credentials for ${D}`),console.log(),console.log(`  IAM Username: ${H.cyan(Q.user.iam_username)}`),Q.user.role==="admin"||Q.user.role==="owner")console.log(`  Access: ${H.magenta("full bucket access (admin/owner)")}`);if(console.log(`  Datasets restored: ${H.green(Q.datasets_restored)}`),Q.warning)console.log(),console.log(H.yellow(`  Warning: ${Q.warning}`)),console.log(H.dim("  Please verify old credentials are revoked in AWS console."));console.log(),console.log(H.dim("The user can now upload to their datasets again."))}catch(Q){eD(Q,J,"Failed to regenerate IAM credentials",{404:"User not found or not approved"})}}var GW=new FD("repo").description("Repository visibility management");GW.command("public").description("Make a dataset repository public").argument("<dataset-id>","Dataset ID (e.g., nm000104)").option(I0,S0).option(a0,g0).action(async(D,F)=>{if(!d0())return;console.log(H.cyan(`
 Making repository public: ${D}
-`)),console.log(H.yellow("Warning: This will make the dataset visible to everyone.")),console.log();let $=await y0(`Make ${D} public?`,F);if($!=="confirmed"){console.log(H.gray($==="declined"?"Skipped":"Cancelled"));return}let J=N(`Setting ${D} to public...`).start();try{await eG(D,"public"),J.succeed(`Repository ${D} is now public`)}catch(Q){eD(Q,J,"Failed to change visibility",{404:"Dataset not found"})}});GW.command("private").description("Make a dataset repository private").argument("<dataset-id>","Dataset ID (e.g., nm000104)").option(I0,S0).option(a0,g0).action(async(D,F)=>{if(!d0())return;console.log(H.yellow(`
+`)),console.log(H.yellow("Warning: This will make the dataset visible to everyone.")),console.log();let $=await y0(`Make ${D} public?`,F);if($!=="confirmed"){console.log(H.dim($==="declined"?"Skipped":"Cancelled"));return}let J=N(`Setting ${D} to public...`).start();try{await eG(D,"public"),J.succeed(`Repository ${D} is now public`)}catch(Q){eD(Q,J,"Failed to change visibility",{404:"Dataset not found"})}});GW.command("private").description("Make a dataset repository private").argument("<dataset-id>","Dataset ID (e.g., nm000104)").option(I0,S0).option(a0,g0).action(async(D,F)=>{if(!d0())return;console.log(H.yellow(`
 Making repository private: ${D}
-`)),console.log("This will restrict access to collaborators only."),console.log();let $=await y0(`Make ${D} private?`,F);if($!=="confirmed"){console.log(H.gray($==="declined"?"Skipped":"Cancelled"));return}let J=N(`Setting ${D} to private...`).start();try{await eG(D,"private"),J.succeed(`Repository ${D} is now private`)}catch(Q){eD(Q,J,"Failed to change visibility",{404:"Dataset not found"})}});KD.addCommand(GW);var WW=new FD("ci").description("CI workflow management");WW.command("check").description("Check CI workflow status for a dataset").argument("<dataset-id>","Dataset ID (e.g., nm000104)").action(async(D)=>{if(!d0())return;let F=N(`Checking CI status for ${D}...`).start();try{let $=await O_(D);F.stop(),console.log(`
+`)),console.log("This will restrict access to collaborators only."),console.log();let $=await y0(`Make ${D} private?`,F);if($!=="confirmed"){console.log(H.dim($==="declined"?"Skipped":"Cancelled"));return}let J=N(`Setting ${D} to private...`).start();try{await eG(D,"private"),J.succeed(`Repository ${D} is now private`)}catch(Q){eD(Q,J,"Failed to change visibility",{404:"Dataset not found"})}});KD.addCommand(GW);var WW=new FD("ci").description("CI workflow management");WW.command("check").description("Check CI workflow status for a dataset").argument("<dataset-id>","Dataset ID (e.g., nm000104)").action(async(D)=>{if(!d0())return;let F=N(`Checking CI status for ${D}...`).start();try{let $=await O_(D);F.stop(),console.log(`
 ${H.cyan("CI Status:")} ${D}
-`);let J=$.bids_validation.present,Q=J?H.green("[x]"):H.red("[ ]");if(console.log(`  ${Q} BIDS Validation`),J){let X=$.bids_validation.status==="success"?H.green:$.bids_validation.status==="failure"?H.red:H.yellow;if(console.log(`      Status: ${X($.bids_validation.status)}`),$.bids_validation.url)console.log(`      URL:    ${H.gray($.bids_validation.url)}`)}else console.log(`      ${H.gray("Not deployed. Use 'nemar admin ci add' to deploy.")}`);let B=$.version_check.present,Y=B?H.green("[x]"):H.red("[ ]");if(console.log(`  ${Y} Version Check`),!B)console.log(`      ${H.gray("Not deployed. Use 'nemar admin ci add' to deploy.")}`);console.log()}catch($){eD($,F,"Failed to check CI status",{404:"Dataset not found"})}});WW.command("add").description("Deploy CI workflows to a dataset repository").argument("<dataset-id>","Dataset ID (e.g., nm000104)").option(I0,S0).option(a0,g0).action(async(D,F)=>{if(!d0())return;console.log(H.cyan(`
+`);let J=$.bids_validation.present,Q=J?H.green("[x]"):H.red("[ ]");if(console.log(`  ${Q} BIDS Validation`),J){let X=$.bids_validation.status==="success"?H.green:$.bids_validation.status==="failure"?H.red:H.yellow;if(console.log(`      Status: ${X($.bids_validation.status)}`),$.bids_validation.url)console.log(`      URL:    ${H.dim($.bids_validation.url)}`)}else console.log(`      ${H.dim("Not deployed. Use 'nemar admin ci add' to deploy.")}`);let B=$.version_check.present,Y=B?H.green("[x]"):H.red("[ ]");if(console.log(`  ${Y} Version Check`),!B)console.log(`      ${H.dim("Not deployed. Use 'nemar admin ci add' to deploy.")}`);console.log()}catch($){eD($,F,"Failed to check CI status",{404:"Dataset not found"})}});WW.command("add").description("Deploy CI workflows to a dataset repository").argument("<dataset-id>","Dataset ID (e.g., nm000104)").option(I0,S0).option(a0,g0).action(async(D,F)=>{if(!d0())return;console.log(H.cyan(`
 Deploy CI workflows to: ${D}
-`)),console.log("This will add the following workflows:"),console.log("  1. BIDS Validation (runs on PRs)"),console.log("  2. Version Check (ensures version bump on PRs)"),console.log("  3. PR Merge Handler (creates releases, publishes DOIs)"),console.log();let $=await y0(`Deploy CI workflows to ${D}?`,F);if($!=="confirmed"){console.log(H.gray($==="declined"?"Skipped":"Cancelled"));return}let J=N(`Deploying CI workflows to ${D}...`).start();try{let Q=await EF(D);J.succeed("CI workflows deployed"),console.log();for(let B of Q.workflows_deployed)console.log(`  ${H.green("[x]")} ${B}`);console.log()}catch(Q){eD(Q,J,"Failed to deploy CI workflows",{404:"Dataset not found"})}});KD.addCommand(WW);var R9=new FD("doi").description("DOI management");R9.command("create").description("Create concept DOI for a dataset").argument("<dataset-id>","Dataset ID (e.g., nm000104)").option("--title <title>","DOI title (defaults to dataset name)").option("--description <desc>","DOI description").option("--provider <provider>","DOI provider: ezid (default) or zenodo","ezid").option("--sandbox","Use sandbox/test DOI").option(I0,S0).option(a0,g0).action(async(D,F)=>{if(!d0())return;let $=N("Fetching dataset info...").start(),J;try{J=await cD(D),$.succeed(`Found dataset: ${J.name}`)}catch(G){if(G instanceof i){if($.fail(G.message),G.statusCode===404)console.log(H.gray("  Dataset not found"))}else $.fail("Failed to fetch dataset");return}try{let G=await Z9(D);if(G.concept_doi){if(console.log(H.yellow(`
-Dataset already has a concept DOI:`)),console.log(`  Concept DOI: ${H.cyan(G.concept_doi)}`),G.zenodo_concept_url)console.log(`  Zenodo URL:  ${G.zenodo_concept_url}`);return}}catch(G){if(process.env.DEBUG)console.error("[debug] DOI info fetch:",G)}if(console.log(),console.log(H.cyan("Dataset Information:")),console.log(`  ID:          ${J.dataset_id}`),console.log(`  Name:        ${J.name}`),J.github_repo)console.log(`  GitHub:      ${J.github_repo}`);if(F.sandbox)console.log(`  Mode:        ${H.yellow("SANDBOX (test DOI)")}`);console.log();let Q=F.provider==="zenodo"?"zenodo":"ezid";if(F.sandbox){if(console.log(H.yellow("\u2501".repeat(60))),console.log(H.yellow.bold("                 SANDBOX MODE ENABLED")),console.log(H.yellow("\u2501".repeat(60))),Q==="zenodo")console.log(H.yellow("  \u2022 Using Zenodo sandbox (sandbox.zenodo.org)"));else console.log(H.yellow("  \u2022 Using EZID test shoulder (doi:10.5072/FK2)")),console.log(H.yellow("  \u2022 Test DOIs auto-delete after 2 weeks"));console.log(H.yellow("  \u2022 DOI will NOT be indexed by DataCite")),console.log(H.yellow("  \u2022 DOI will NOT resolve in production")),console.log(H.yellow("  \u2022 Use this for testing workflows only")),console.log(H.yellow("\u2501".repeat(60))),console.log()}console.log(H.red("WARNING: DOIs are PERMANENT and cannot be deleted!")),console.log(H.gray("The DOI will be pre-reserved but not published until the first version release.")),console.log(`  Provider: ${H.cyan(Q.toUpperCase())}`),console.log();let B=F.sandbox?`Create TEST concept DOI via ${Q.toUpperCase()} SANDBOX?`:`Create PERMANENT concept DOI via ${Q.toUpperCase()} PRODUCTION?`,Y=await y0(B,F);if(Y!=="confirmed"){console.log(H.gray(Y==="declined"?"Skipped":"Cancelled"));return}let X=N(`Creating concept DOI via ${Q.toUpperCase()}...`).start();try{let G=await k_(D,{title:F.title,description:F.description,sandbox:F.sandbox,provider:Q});X.succeed("Concept DOI created successfully");let W=N("Applying branch protection...").start();try{let q=await fJ(D);if(q.warnings&&q.warnings.length>0){W.warn("Branch protection applied with warnings");for(let K of q.warnings)console.log(H.yellow(`  Warning: ${K}`))}else W.succeed("Branch protection applied")}catch(q){if(W.warn("Could not apply branch protection"),q instanceof i){if(console.log(H.gray(`  ${q.message}`)),q.statusCode===403)console.log(H.gray("  Check admin credentials and permissions"))}else console.log(H.gray(`  ${q instanceof Error?q.message:"Unknown error"}`));console.log(H.gray("  Manual setup: Go to GitHub repo Settings > Branches > Add rule"))}if(console.log(),console.log(H.green("DOI Information:")),console.log(`  Concept DOI: ${H.cyan(G.concept_doi)}`),console.log(`  Provider:    ${G.provider.toUpperCase()}`),G.provider==="ezid")console.log(`  DOI URL:     ${G.doi_url}`),console.log(`  EZID ID:     ${G.ezid_identifier}`);else console.log(`  Zenodo URL:  ${G.zenodo_url}`);if(G.metadata_warning)console.log(H.yellow(`  Warning:     ${G.metadata_warning}`));if(console.log(),console.log(H.yellow("Next steps:")),console.log("  1. Update dataset_description.json with DatasetDOI field"),console.log("  2. Create a PR and merge it to trigger version DOI publication"),console.log(),F.sandbox)console.log(H.gray("Note: This is a sandbox DOI and will not resolve in production."))}catch(G){if(G instanceof i){if(X.fail(G.message),G.statusCode===403)console.log(H.gray("  This command requires admin privileges"))}else X.fail("Failed to create concept DOI"),console.log(H.gray(`  ${p0(G)}`))}});R9.command("info").description("Get DOI info for a dataset").argument("<dataset-id>","Dataset ID (e.g., nm000104)").action(async(D)=>{if(!d0())return;let F=N("Fetching DOI info...").start();try{let $=await Z9(D);if(F.stop(),console.log(),console.log(H.cyan(`DOI Information for ${D}:`)),console.log(`  Dataset Name:    ${$.name}`),console.log(),$.concept_doi){if(console.log(H.green("Concept DOI:")),console.log(`  DOI:      ${$.concept_doi}`),console.log(`  URL:      https://doi.org/${$.concept_doi}`),console.log(`  Provider: ${($.doi_provider||"zenodo").toUpperCase()}`),$.doi_provider==="ezid"){if($.ezid_identifier)console.log(`  EZID ID:  ${$.ezid_identifier}`);if($.ezid_status){let J=$.ezid_status==="public"?H.green:H.yellow;console.log(`  Status:   ${J($.ezid_status)}`)}}if($.zenodo_concept_url){if(console.log(`  Zenodo:   ${$.zenodo_concept_url}`),$.zenodo_concept_url.includes("sandbox.zenodo.org"))console.log(),console.log(H.yellow("Mode: SANDBOX (test DOI)")),console.log(H.yellow("  This DOI is not indexed by DataCite and will not resolve in production"))}}else console.log(H.yellow("No concept DOI created yet")),console.log(H.gray("  Use 'nemar admin doi create' to create one"));if(console.log(),$.latest_version_doi){if(console.log(H.green("Latest Version DOI:")),console.log(`  DOI:  ${$.latest_version_doi}`),console.log(`  URL:  https://doi.org/${$.latest_version_doi}`),$.zenodo_latest_version_url)console.log(`  Zenodo: ${$.zenodo_latest_version_url}`)}else if($.concept_doi)console.log(H.yellow("No version DOI published yet")),console.log(H.gray("  Version DOIs are created automatically on PR merge"))}catch($){if($ instanceof i){if(F.fail($.message),$.statusCode===404)console.log(H.gray("  Dataset not found"));else if($.statusCode===403)console.log(H.gray("  This command requires admin privileges"))}else F.fail("Failed to fetch DOI info")}});R9.command("update").description("Update EZID DOI metadata or status").argument("<dataset-id>","Dataset ID (e.g., nm000104)").option("--make-public","Transition DOI from reserved to public (permanent)").option("--refresh","Refresh metadata from dataset_description.json and .nemar/metadata.json").option(I0,S0).option(a0,g0).action(async(D,F)=>{if(!d0())return;if(!F.makePublic&&!F.refresh){console.log(H.yellow("No action specified. Use --make-public and/or --refresh."));return}if(F.makePublic){console.log(H.red("WARNING: Making a DOI public is PERMANENT!")),console.log(H.gray("  The DOI will be findable in DataCite and cannot be reverted.")),console.log();let J=await y0(`Make DOI for ${D} PUBLIC and permanent?`,F);if(J!=="confirmed"){console.log(H.gray(J==="declined"?"Skipped":"Cancelled"));return}}let $=N("Updating DOI...").start();try{let J=await DW(D,{status:F.makePublic?"public":void 0,refresh_metadata:F.refresh});$.succeed("DOI updated successfully"),console.log(),console.log(`  EZID ID: ${H.cyan(J.ezid_identifier)}`),console.log(`  Status:  ${J.status==="public"?H.green(J.status):H.yellow(J.status)}`),console.log(`  URL:     ${J.doi_url}`)}catch(J){if(J instanceof i){if($.fail(J.message),J.statusCode===400)console.log(H.gray("  DOI update is only supported for EZID-managed DOIs"))}else $.fail("Failed to update DOI"),console.log(H.gray(`  ${p0(J)}`))}});R9.command("enrich").description("Enrich DOI metadata with ORCIDs, descriptions, funding, and more").argument("<dataset-id>","Dataset ID (e.g., nm000104)").option("--no-llm","Skip LLM-based enrichment from README").option("--sandbox","Use sandbox DOI").option(I0,S0).option(a0,g0).action(async(D,F)=>{if(!d0())return;let $=N("Fetching dataset and existing enrichment...").start(),J;try{J=await cD(D),$.succeed(`Dataset: ${J.name}`)}catch(z){if(z instanceof i)$.fail(z.message);else $.fail("Failed to fetch dataset");return}let Q,B=!1;try{Q=await Z9(D)}catch(z){if(z instanceof i&&z.statusCode===404);else B=!0,console.log(H.yellow(`  Warning: Could not fetch DOI info: ${p0(z)}`))}if(Q?.concept_doi)console.log(`  DOI: ${H.cyan(Q.concept_doi)}`);let Y={version:"2.0"};if(J.github_repo){let z=N("Reading existing metadata...").start(),U=await vf(J.github_repo,".nemar/metadata.json");if(U)try{let A=JSON.parse(U);if(A&&typeof A==="object"&&A.version==="2.0")Y=A,z.succeed(`Loaded existing metadata (stage: ${A.pipeline_stage||"unknown"})`);else z.warn("Existing metadata has unsupported version, starting fresh")}catch(A){z.warn(`Could not parse existing metadata (${A instanceof Error?A.message:String(A)}), starting fresh`)}else z.info("No existing .nemar/metadata.json found, starting fresh")}if(F.llm!==!1&&J.github_repo){console.log(),console.log(H.cyan("--- Running LLM enrichment pipeline (CI workflow) ---"));let z=N("Triggering llm-enrichment workflow...").start();try{let{spawn:U}=awaitPromise.resolve(globalThis.Bun),A=J.github_repo,M=U({cmd:["gh","workflow","run","llm-enrichment.yml","--repo",A,"--ref","main"],stdout:"pipe",stderr:"pipe"}),L=await new Response(M.stderr).text();if(await M.exited!==0)throw Error(`Failed to trigger workflow: ${L.trim()}`);z.text="Waiting for workflow to register...",await new Promise((T)=>setTimeout(T,3000)),z.text="Polling workflow status...";let O=60,y="",w=0;for(let T=0;T<O;T++){let f=U({cmd:["gh","run","list","--repo",A,"--workflow","llm-enrichment.yml","-L","1","--json","databaseId,status,conclusion"],stdout:"pipe",stderr:"pipe"}),n=await new Response(f.stdout).text(),s=await new Response(f.stderr).text();if(await f.exited!==0){if(w++,w>=3){z.warn(`gh CLI error: ${s.trim()}`);break}await new Promise((t)=>setTimeout(t,5000));continue}try{let t=JSON.parse(n.trim());if(w=0,t.length>0){let t0=t[0];if(t0.status==="completed"){y=t0.conclusion||"unknown";break}z.text=`Workflow ${t0.status}... (${T*5}s)`}}catch(t){if(w++,w>=3){z.warn(`Unable to parse workflow status: ${t instanceof Error?t.message:String(t)} (raw: ${n.trim().slice(0,200)})`);break}}await new Promise((t)=>setTimeout(t,5000))}let I=!1;if(!y)z.warn("Workflow timed out after 5 minutes (may still be running)");else if(y==="success"){z.succeed("LLM enrichment workflow completed successfully");let T=await vf(A,".nemar/metadata.json");if(T)try{let f=JSON.parse(T);if(f&&typeof f==="object"&&f.version==="2.0"){Object.assign(Y,f),I=!0;let n=f.pipeline_stage||"unknown";if(console.log(H.gray(`  Pipeline stage: ${n}`)),Y.authors){let s=Object.keys(Y.authors).length;console.log(H.gray(`  Authors: ${s}`))}}}catch(f){console.log(H.yellow(`  Warning: Could not parse updated metadata: ${f instanceof Error?f.message:String(f)}`)),console.log(H.gray("  Using pre-workflow enrichment data"))}else console.log(H.yellow("  Warning: Could not fetch updated metadata after successful workflow.")),console.log(H.gray("  Author data below may be from a previous run."))}else z.fail(`LLM enrichment workflow failed (conclusion: ${y})`);if(!I)console.log(H.yellow("  ORCID discovery did not complete. Authors below may be from previous metadata."))}catch(U){z.fail("LLM enrichment pipeline failed"),console.log(H.gray(`  ${p0(U)}`)),console.log(H.yellow("  ORCID discovery did not run. You will need to enter ORCIDs manually."))}}console.log(),console.log(H.cyan("--- Author ORCIDs ---"));let X=Y.authors||{},G=Object.keys(X);if(G.length>0){let z=G.filter((A)=>X[A]?.orcid),U=G.filter((A)=>!X[A]?.orcid);console.log(H.gray(`  Discovered ${G.length} authors from pipeline:`));for(let A of z)console.log(H.green(`    [x] ${A}: ${X[A]?.orcid}`));for(let A of U)console.log(H.yellow(`    [ ] ${A}: no ORCID found`));if(U.length>0)console.log(H.gray(`  ${U.length} author(s) missing ORCIDs.`))}let{updateAuthors:W}=await B0.prompt([{type:"confirm",name:"updateAuthors",message:G.length>0?"Add or correct author ORCIDs?":"Add author ORCIDs manually?",default:!1}]);if(W){let z={},U=!0;while(U){let{authorName:A}=await B0.prompt([{type:"input",name:"authorName",message:'Author name (as in BIDS, e.g., "Shirazi, Yahya"):'}]);if(!A)break;let M=X[A];if(M?.orcid)console.log(H.gray(`  Current ORCID: ${M.orcid}`));let{orcid:L}=await B0.prompt([{type:"input",name:"orcid",message:`ORCID for "${A}" (Enter to ${M?.orcid?"keep current":"skip"}):`,validate:(w)=>{if(!w)return!0;return yJ.test(w)||"Invalid ORCID format (XXXX-XXXX-XXXX-XXXX)"}}]),C={};if(L)C.orcid=L;let{affiliation:O}=await B0.prompt([{type:"input",name:"affiliation",message:`Affiliation for "${A}" (optional):`}]);if(O)C.affiliations=[{name:O}];if(C.orcid||C.affiliations)z[A]=C;let{more:y}=await B0.prompt([{type:"confirm",name:"more",message:"Add another author?",default:!0}]);U=y}if(Object.keys(z).length>0){let A={...Y.authors||{}};for(let[M,L]of Object.entries(z)){let C=A[M]||{};A[M]={...C,...L,orcid:L.orcid||C.orcid}}Y.authors=A}}console.log(),console.log(H.cyan("--- Dataset stats ---"));let q=N("Computing dataset sizes and formats...").start();try{let z=await p_(D),U=V8(z.total_size);Y.sizes=[`${U} (${z.file_count} files)`],Y.formats=z.extensions,q.succeed(`Sizes: ${U} (${z.file_count} files), Formats: ${z.extensions.join(", ")}`)}catch(z){q.warn("Could not compute dataset stats"),console.log(H.gray(`  ${p0(z)}`))}console.log(),console.log(H.cyan("--- Review ---")),console.log(JSON.stringify(Y,null,2)),console.log();let K=await y0("Commit to repo and refresh DOI?",F,!0);if(K!=="confirmed"){console.log(H.gray(K==="declined"?"Skipped":"Cancelled"));return}let Z=N("Saving enrichment...").start();try{let z=await l_(D,Y);if(Z.succeed(z.message),z.bidsignore_updated)console.log(H.gray("  .bidsignore updated to include .nemar/"));if(!Q&&B)try{Q=await Z9(D)}catch(U){if(process.env.DEBUG)console.error("[debug] DOI info re-fetch:",U)}if(Q?.ezid_identifier){let U=N("Refreshing DOI metadata...").start();try{await DW(D,{refresh_metadata:!0}),U.succeed("DOI metadata refreshed")}catch(A){U.warn("Could not refresh DOI metadata"),console.log(H.gray(`  ${p0(A)}`))}}else if(B)console.log(H.yellow("  DOI refresh skipped: could not verify DOI exists. Run 'nemar admin doi update --refresh' manually."))}catch(z){if(z instanceof i)Z.fail(z.message);else Z.fail("Failed to save enrichment"),console.log(H.gray(`  ${p0(z)}`))}});KD.addCommand(R9);var dJ=new FD("publish").description("Publication workflow management");dJ.command("list").description("List publication requests").option("-s, --status <status>","Filter by status (requested, approving, published, denied)").addHelpText("after",`
+`)),console.log("This will add the following workflows:"),console.log("  1. BIDS Validation (runs on PRs)"),console.log("  2. Version Check (ensures version bump on PRs)"),console.log("  3. PR Merge Handler (creates releases, publishes DOIs)"),console.log();let $=await y0(`Deploy CI workflows to ${D}?`,F);if($!=="confirmed"){console.log(H.dim($==="declined"?"Skipped":"Cancelled"));return}let J=N(`Deploying CI workflows to ${D}...`).start();try{let Q=await EF(D);J.succeed("CI workflows deployed"),console.log();for(let B of Q.workflows_deployed)console.log(`  ${H.green("[x]")} ${B}`);console.log()}catch(Q){eD(Q,J,"Failed to deploy CI workflows",{404:"Dataset not found"})}});KD.addCommand(WW);var R9=new FD("doi").description("DOI management");R9.command("create").description("Create concept DOI for a dataset").argument("<dataset-id>","Dataset ID (e.g., nm000104)").option("--title <title>","DOI title (defaults to dataset name)").option("--description <desc>","DOI description").option("--provider <provider>","DOI provider: ezid (default) or zenodo","ezid").option("--sandbox","Use sandbox/test DOI").option(I0,S0).option(a0,g0).action(async(D,F)=>{if(!d0())return;let $=N("Fetching dataset info...").start(),J;try{J=await cD(D),$.succeed(`Found dataset: ${J.name}`)}catch(G){if(G instanceof i){if($.fail(G.message),G.statusCode===404)console.log(H.dim("  Dataset not found"))}else $.fail("Failed to fetch dataset");return}try{let G=await Z9(D);if(G.concept_doi){if(console.log(H.yellow(`
+Dataset already has a concept DOI:`)),console.log(`  Concept DOI: ${H.cyan(G.concept_doi)}`),G.zenodo_concept_url)console.log(`  Zenodo URL:  ${G.zenodo_concept_url}`);return}}catch(G){if(process.env.DEBUG)console.error("[debug] DOI info fetch:",G)}if(console.log(),console.log(H.cyan("Dataset Information:")),console.log(`  ID:          ${J.dataset_id}`),console.log(`  Name:        ${J.name}`),J.github_repo)console.log(`  GitHub:      ${J.github_repo}`);if(F.sandbox)console.log(`  Mode:        ${H.yellow("SANDBOX (test DOI)")}`);console.log();let Q=F.provider==="zenodo"?"zenodo":"ezid";if(F.sandbox){if(console.log(H.yellow("\u2501".repeat(60))),console.log(H.yellow.bold("                 SANDBOX MODE ENABLED")),console.log(H.yellow("\u2501".repeat(60))),Q==="zenodo")console.log(H.yellow("  \u2022 Using Zenodo sandbox (sandbox.zenodo.org)"));else console.log(H.yellow("  \u2022 Using EZID test shoulder (doi:10.5072/FK2)")),console.log(H.yellow("  \u2022 Test DOIs auto-delete after 2 weeks"));console.log(H.yellow("  \u2022 DOI will NOT be indexed by DataCite")),console.log(H.yellow("  \u2022 DOI will NOT resolve in production")),console.log(H.yellow("  \u2022 Use this for testing workflows only")),console.log(H.yellow("\u2501".repeat(60))),console.log()}console.log(H.red("WARNING: DOIs are PERMANENT and cannot be deleted!")),console.log(H.dim("The DOI will be pre-reserved but not published until the first version release.")),console.log(`  Provider: ${H.cyan(Q.toUpperCase())}`),console.log();let B=F.sandbox?`Create TEST concept DOI via ${Q.toUpperCase()} SANDBOX?`:`Create PERMANENT concept DOI via ${Q.toUpperCase()} PRODUCTION?`,Y=await y0(B,F);if(Y!=="confirmed"){console.log(H.dim(Y==="declined"?"Skipped":"Cancelled"));return}let X=N(`Creating concept DOI via ${Q.toUpperCase()}...`).start();try{let G=await k_(D,{title:F.title,description:F.description,sandbox:F.sandbox,provider:Q});X.succeed("Concept DOI created successfully");let W=N("Applying branch protection...").start();try{let q=await fJ(D);if(q.warnings&&q.warnings.length>0){W.warn("Branch protection applied with warnings");for(let K of q.warnings)console.log(H.yellow(`  Warning: ${K}`))}else W.succeed("Branch protection applied")}catch(q){if(W.warn("Could not apply branch protection"),q instanceof i){if(console.log(H.dim(`  ${q.message}`)),q.statusCode===403)console.log(H.dim("  Check admin credentials and permissions"))}else console.log(H.dim(`  ${q instanceof Error?q.message:"Unknown error"}`));console.log(H.dim("  Manual setup: Go to GitHub repo Settings > Branches > Add rule"))}if(console.log(),console.log(H.green("DOI Information:")),console.log(`  Concept DOI: ${H.cyan(G.concept_doi)}`),console.log(`  Provider:    ${G.provider.toUpperCase()}`),G.provider==="ezid")console.log(`  DOI URL:     ${G.doi_url}`),console.log(`  EZID ID:     ${G.ezid_identifier}`);else console.log(`  Zenodo URL:  ${G.zenodo_url}`);if(G.metadata_warning)console.log(H.yellow(`  Warning:     ${G.metadata_warning}`));if(console.log(),console.log(H.yellow("Next steps:")),console.log("  1. Update dataset_description.json with DatasetDOI field"),console.log("  2. Create a PR and merge it to trigger version DOI publication"),console.log(),F.sandbox)console.log(H.dim("Note: This is a sandbox DOI and will not resolve in production."))}catch(G){if(G instanceof i){if(X.fail(G.message),G.statusCode===403)console.log(H.dim("  This command requires admin privileges"))}else X.fail("Failed to create concept DOI"),console.log(H.dim(`  ${p0(G)}`))}});R9.command("info").description("Get DOI info for a dataset").argument("<dataset-id>","Dataset ID (e.g., nm000104)").action(async(D)=>{if(!d0())return;let F=N("Fetching DOI info...").start();try{let $=await Z9(D);if(F.stop(),console.log(),console.log(H.cyan(`DOI Information for ${D}:`)),console.log(`  Dataset Name:    ${$.name}`),console.log(),$.concept_doi){if(console.log(H.green("Concept DOI:")),console.log(`  DOI:      ${$.concept_doi}`),console.log(`  URL:      https://doi.org/${$.concept_doi}`),console.log(`  Provider: ${($.doi_provider||"zenodo").toUpperCase()}`),$.doi_provider==="ezid"){if($.ezid_identifier)console.log(`  EZID ID:  ${$.ezid_identifier}`);if($.ezid_status){let J=$.ezid_status==="public"?H.green:H.yellow;console.log(`  Status:   ${J($.ezid_status)}`)}}if($.zenodo_concept_url){if(console.log(`  Zenodo:   ${$.zenodo_concept_url}`),$.zenodo_concept_url.includes("sandbox.zenodo.org"))console.log(),console.log(H.yellow("Mode: SANDBOX (test DOI)")),console.log(H.yellow("  This DOI is not indexed by DataCite and will not resolve in production"))}}else console.log(H.yellow("No concept DOI created yet")),console.log(H.dim("  Use 'nemar admin doi create' to create one"));if(console.log(),$.latest_version_doi){if(console.log(H.green("Latest Version DOI:")),console.log(`  DOI:  ${$.latest_version_doi}`),console.log(`  URL:  https://doi.org/${$.latest_version_doi}`),$.zenodo_latest_version_url)console.log(`  Zenodo: ${$.zenodo_latest_version_url}`)}else if($.concept_doi)console.log(H.yellow("No version DOI published yet")),console.log(H.dim("  Version DOIs are created automatically on PR merge"))}catch($){if($ instanceof i){if(F.fail($.message),$.statusCode===404)console.log(H.dim("  Dataset not found"));else if($.statusCode===403)console.log(H.dim("  This command requires admin privileges"))}else F.fail("Failed to fetch DOI info")}});R9.command("update").description("Update EZID DOI metadata or status").argument("<dataset-id>","Dataset ID (e.g., nm000104)").option("--make-public","Transition DOI from reserved to public (permanent)").option("--refresh","Refresh metadata from dataset_description.json and .nemar/metadata.json").option(I0,S0).option(a0,g0).action(async(D,F)=>{if(!d0())return;if(!F.makePublic&&!F.refresh){console.log(H.yellow("No action specified. Use --make-public and/or --refresh."));return}if(F.makePublic){console.log(H.red("WARNING: Making a DOI public is PERMANENT!")),console.log(H.dim("  The DOI will be findable in DataCite and cannot be reverted.")),console.log();let J=await y0(`Make DOI for ${D} PUBLIC and permanent?`,F);if(J!=="confirmed"){console.log(H.dim(J==="declined"?"Skipped":"Cancelled"));return}}let $=N("Updating DOI...").start();try{let J=await DW(D,{status:F.makePublic?"public":void 0,refresh_metadata:F.refresh});$.succeed("DOI updated successfully"),console.log(),console.log(`  EZID ID: ${H.cyan(J.ezid_identifier)}`),console.log(`  Status:  ${J.status==="public"?H.green(J.status):H.yellow(J.status)}`),console.log(`  URL:     ${J.doi_url}`)}catch(J){if(J instanceof i){if($.fail(J.message),J.statusCode===400)console.log(H.dim("  DOI update is only supported for EZID-managed DOIs"))}else $.fail("Failed to update DOI"),console.log(H.dim(`  ${p0(J)}`))}});R9.command("enrich").description("Enrich DOI metadata with ORCIDs, descriptions, funding, and more").argument("<dataset-id>","Dataset ID (e.g., nm000104)").option("--no-llm","Skip LLM-based enrichment from README").option("--sandbox","Use sandbox DOI").option(I0,S0).option(a0,g0).action(async(D,F)=>{if(!d0())return;let $=N("Fetching dataset and existing enrichment...").start(),J;try{J=await cD(D),$.succeed(`Dataset: ${J.name}`)}catch(z){if(z instanceof i)$.fail(z.message);else $.fail("Failed to fetch dataset");return}let Q,B=!1;try{Q=await Z9(D)}catch(z){if(z instanceof i&&z.statusCode===404);else B=!0,console.log(H.yellow(`  Warning: Could not fetch DOI info: ${p0(z)}`))}if(Q?.concept_doi)console.log(`  DOI: ${H.cyan(Q.concept_doi)}`);let Y={version:"2.0"};if(J.github_repo){let z=N("Reading existing metadata...").start(),U=await vf(J.github_repo,".nemar/metadata.json");if(U)try{let A=JSON.parse(U);if(A&&typeof A==="object"&&A.version==="2.0")Y=A,z.succeed(`Loaded existing metadata (stage: ${A.pipeline_stage||"unknown"})`);else z.warn("Existing metadata has unsupported version, starting fresh")}catch(A){z.warn(`Could not parse existing metadata (${A instanceof Error?A.message:String(A)}), starting fresh`)}else z.info("No existing .nemar/metadata.json found, starting fresh")}if(F.llm!==!1&&J.github_repo){console.log(),console.log(H.cyan("--- Running LLM enrichment pipeline (CI workflow) ---"));let z=N("Triggering llm-enrichment workflow...").start();try{let{spawn:U}=awaitPromise.resolve(globalThis.Bun),A=J.github_repo,M=U({cmd:["gh","workflow","run","llm-enrichment.yml","--repo",A,"--ref","main"],stdout:"pipe",stderr:"pipe"}),L=await new Response(M.stderr).text();if(await M.exited!==0)throw Error(`Failed to trigger workflow: ${L.trim()}`);z.text="Waiting for workflow to register...",await new Promise((T)=>setTimeout(T,3000)),z.text="Polling workflow status...";let O=60,y="",w=0;for(let T=0;T<O;T++){let f=U({cmd:["gh","run","list","--repo",A,"--workflow","llm-enrichment.yml","-L","1","--json","databaseId,status,conclusion"],stdout:"pipe",stderr:"pipe"}),n=await new Response(f.stdout).text(),s=await new Response(f.stderr).text();if(await f.exited!==0){if(w++,w>=3){z.warn(`gh CLI error: ${s.trim()}`);break}await new Promise((t)=>setTimeout(t,5000));continue}try{let t=JSON.parse(n.trim());if(w=0,t.length>0){let t0=t[0];if(t0.status==="completed"){y=t0.conclusion||"unknown";break}z.text=`Workflow ${t0.status}... (${T*5}s)`}}catch(t){if(w++,w>=3){z.warn(`Unable to parse workflow status: ${t instanceof Error?t.message:String(t)} (raw: ${n.trim().slice(0,200)})`);break}}await new Promise((t)=>setTimeout(t,5000))}let I=!1;if(!y)z.warn("Workflow timed out after 5 minutes (may still be running)");else if(y==="success"){z.succeed("LLM enrichment workflow completed successfully");let T=await vf(A,".nemar/metadata.json");if(T)try{let f=JSON.parse(T);if(f&&typeof f==="object"&&f.version==="2.0"){Object.assign(Y,f),I=!0;let n=f.pipeline_stage||"unknown";if(console.log(H.dim(`  Pipeline stage: ${n}`)),Y.authors){let s=Object.keys(Y.authors).length;console.log(H.dim(`  Authors: ${s}`))}}}catch(f){console.log(H.yellow(`  Warning: Could not parse updated metadata: ${f instanceof Error?f.message:String(f)}`)),console.log(H.dim("  Using pre-workflow enrichment data"))}else console.log(H.yellow("  Warning: Could not fetch updated metadata after successful workflow.")),console.log(H.dim("  Author data below may be from a previous run."))}else z.fail(`LLM enrichment workflow failed (conclusion: ${y})`);if(!I)console.log(H.yellow("  ORCID discovery did not complete. Authors below may be from previous metadata."))}catch(U){z.fail("LLM enrichment pipeline failed"),console.log(H.dim(`  ${p0(U)}`)),console.log(H.yellow("  ORCID discovery did not run. You will need to enter ORCIDs manually."))}}console.log(),console.log(H.cyan("--- Author ORCIDs ---"));let X=Y.authors||{},G=Object.keys(X);if(G.length>0){let z=G.filter((A)=>X[A]?.orcid),U=G.filter((A)=>!X[A]?.orcid);console.log(H.dim(`  Discovered ${G.length} authors from pipeline:`));for(let A of z)console.log(H.green(`    [x] ${A}: ${X[A]?.orcid}`));for(let A of U)console.log(H.yellow(`    [ ] ${A}: no ORCID found`));if(U.length>0)console.log(H.dim(`  ${U.length} author(s) missing ORCIDs.`))}let{updateAuthors:W}=await B0.prompt([{type:"confirm",name:"updateAuthors",message:G.length>0?"Add or correct author ORCIDs?":"Add author ORCIDs manually?",default:!1}]);if(W){let z={},U=!0;while(U){let{authorName:A}=await B0.prompt([{type:"input",name:"authorName",message:'Author name (as in BIDS, e.g., "Shirazi, Yahya"):'}]);if(!A)break;let M=X[A];if(M?.orcid)console.log(H.dim(`  Current ORCID: ${M.orcid}`));let{orcid:L}=await B0.prompt([{type:"input",name:"orcid",message:`ORCID for "${A}" (Enter to ${M?.orcid?"keep current":"skip"}):`,validate:(w)=>{if(!w)return!0;return yJ.test(w)||"Invalid ORCID format (XXXX-XXXX-XXXX-XXXX)"}}]),C={};if(L)C.orcid=L;let{affiliation:O}=await B0.prompt([{type:"input",name:"affiliation",message:`Affiliation for "${A}" (optional):`}]);if(O)C.affiliations=[{name:O}];if(C.orcid||C.affiliations)z[A]=C;let{more:y}=await B0.prompt([{type:"confirm",name:"more",message:"Add another author?",default:!0}]);U=y}if(Object.keys(z).length>0){let A={...Y.authors||{}};for(let[M,L]of Object.entries(z)){let C=A[M]||{};A[M]={...C,...L,orcid:L.orcid||C.orcid}}Y.authors=A}}console.log(),console.log(H.cyan("--- Dataset stats ---"));let q=N("Computing dataset sizes and formats...").start();try{let z=await p_(D),U=V8(z.total_size);Y.sizes=[`${U} (${z.file_count} files)`],Y.formats=z.extensions,q.succeed(`Sizes: ${U} (${z.file_count} files), Formats: ${z.extensions.join(", ")}`)}catch(z){q.warn("Could not compute dataset stats"),console.log(H.dim(`  ${p0(z)}`))}console.log(),console.log(H.cyan("--- Review ---")),console.log(JSON.stringify(Y,null,2)),console.log();let K=await y0("Commit to repo and refresh DOI?",F,!0);if(K!=="confirmed"){console.log(H.dim(K==="declined"?"Skipped":"Cancelled"));return}let Z=N("Saving enrichment...").start();try{let z=await l_(D,Y);if(Z.succeed(z.message),z.bidsignore_updated)console.log(H.dim("  .bidsignore updated to include .nemar/"));if(!Q&&B)try{Q=await Z9(D)}catch(U){if(process.env.DEBUG)console.error("[debug] DOI info re-fetch:",U)}if(Q?.ezid_identifier){let U=N("Refreshing DOI metadata...").start();try{await DW(D,{refresh_metadata:!0}),U.succeed("DOI metadata refreshed")}catch(A){U.warn("Could not refresh DOI metadata"),console.log(H.dim(`  ${p0(A)}`))}}else if(B)console.log(H.yellow("  DOI refresh skipped: could not verify DOI exists. Run 'nemar admin doi update --refresh' manually."))}catch(z){if(z instanceof i)Z.fail(z.message);else Z.fail("Failed to save enrichment"),console.log(H.dim(`  ${p0(z)}`))}});KD.addCommand(R9);var dJ=new FD("publish").description("Publication workflow management");dJ.command("list").description("List publication requests").option("-s, --status <status>","Filter by status (requested, approving, published, denied)").addHelpText("after",`
 Description:
   List all publication requests from users, with optional filtering by status.
   Shows dataset ID, status, requesting user, and current progress.
@@ -207,11 +207,11 @@ Examples:
   $ nemar admin publish list                # All requests
   $ nemar admin publish list --status requested   # Pending only
   $ nemar admin publish list --status approving   # In progress
-  $ nemar admin publish list --status denied      # View denied`).action(async(D)=>{if(!d0())return;let F=N("Fetching publication requests...").start();try{let $=await u_(D.status);if(F.stop(),$.requests.length===0){console.log(H.gray(`
+  $ nemar admin publish list --status denied      # View denied`).action(async(D)=>{if(!d0())return;let F=N("Fetching publication requests...").start();try{let $=await u_(D.status);if(F.stop(),$.requests.length===0){console.log(H.dim(`
   No publication requests found.
 `));return}console.log(`
 ${H.cyan("Publication Requests")} (${$.count})
-`);for(let J of $.requests){let Q=J.status==="published"?H.green:J.status==="denied"?H.red:J.status==="approving"?H.yellow:H.white;if(console.log(`  ${H.bold(J.dataset_id)}  ${Q(J.status)}  by ${J.requested_by_username}  ${H.gray(J.requested_at)}`),J.current_step&&J.status==="approving")console.log(`    ${H.yellow(">")} ${J.current_step.replace(/_/g," ")}${J.last_error?H.red(` (${J.last_error})`):""}`)}console.log()}catch($){eD($,F,"Failed to list publication requests")}});dJ.command("deny").description("Deny a publication request").argument("<dataset-id>","Dataset ID").option("-r, --reason <reason>","Reason for denial").option(I0,S0).option(a0,g0).addHelpText("after",`
+`);for(let J of $.requests){let Q=J.status==="published"?H.green:J.status==="denied"?H.red:J.status==="approving"?H.yellow:H.white;if(console.log(`  ${H.bold(J.dataset_id)}  ${Q(J.status)}  by ${J.requested_by_username}  ${H.dim(J.requested_at)}`),J.current_step&&J.status==="approving")console.log(`    ${H.yellow(">")} ${J.current_step.replace(/_/g," ")}${J.last_error?H.red(` (${J.last_error})`):""}`)}console.log()}catch($){eD($,F,"Failed to list publication requests")}});dJ.command("deny").description("Deny a publication request").argument("<dataset-id>","Dataset ID").option("-r, --reason <reason>","Reason for denial").option(I0,S0).option(a0,g0).addHelpText("after",`
 Description:
   Deny a user's publication request with a specific reason.
   The user will receive an email notification with your reason.
@@ -227,7 +227,7 @@ Requirements:
 Examples:
   $ nemar admin publish deny nm000104 --reason "BIDS validation failing"
   $ nemar admin publish deny nm000104 -r "Dataset incomplete - missing subjects"
-  $ nemar admin publish deny nm000104    # Prompts for reason interactively`).action(async(D,F)=>{if(!d0())return;let $=F.reason;if(!$){let{inputReason:B}=await B0.prompt([{type:"input",name:"inputReason",message:"Reason for denial:"}]);$=B}if(!$){console.log(H.red("Reason is required"));return}let J=await y0(`Deny publication of ${D}?`,F);if(J!=="confirmed"){console.log(H.gray(J==="declined"?"Skipped":"Cancelled"));return}let Q=N(`Denying publication for ${D}...`).start();try{await m_(D,$),Q.succeed(`Publication denied for ${D}`),console.log(H.gray("  User has been notified."))}catch(B){eD(B,Q,"Failed to deny publication")}});dJ.command("approve").description("Approve and publish a dataset (runs orchestrator)").argument("<dataset-id>","Dataset ID").option("--resume","Resume from last failed step").option("--sandbox","Use Zenodo sandbox for testing").option("--skip-ci-check","Skip BIDS validation CI check (admin override)").option(I0,S0).option(a0,g0).addHelpText("after",`
+  $ nemar admin publish deny nm000104    # Prompts for reason interactively`).action(async(D,F)=>{if(!d0())return;let $=F.reason;if(!$){let{inputReason:B}=await B0.prompt([{type:"input",name:"inputReason",message:"Reason for denial:"}]);$=B}if(!$){console.log(H.red("Reason is required"));return}let J=await y0(`Deny publication of ${D}?`,F);if(J!=="confirmed"){console.log(H.dim(J==="declined"?"Skipped":"Cancelled"));return}let Q=N(`Denying publication for ${D}...`).start();try{await m_(D,$),Q.succeed(`Publication denied for ${D}`),console.log(H.dim("  User has been notified."))}catch(B){eD(B,Q,"Failed to deny publication")}});dJ.command("approve").description("Approve and publish a dataset (runs orchestrator)").argument("<dataset-id>","Dataset ID").option("--resume","Resume from last failed step").option("--sandbox","Use Zenodo sandbox for testing").option("--skip-ci-check","Skip BIDS validation CI check (admin override)").option(I0,S0).option(a0,g0).addHelpText("after",`
 Description:
   Approve a publication request and run the automated 15-step orchestrator
   to make the dataset publicly accessible with a permanent DOI.
@@ -271,17 +271,17 @@ After Approval:
   - Tags are protected (prevents version manipulation)
   - Data is protected by S3 Object Lock`).action(async(D,F)=>{if(!d0())return;let $=F.resume?`Resume publication of ${D}`:`Approve and publish ${D}`;if(console.log(H.cyan(`
 ${$}
-`)),console.log("This will run the following 15-step orchestrator:"),console.log("   1. Check CI              9. Create version tag"),console.log("   2. Enrichment check     10. Create GitHub release"),console.log("   3. Make repo public     11. Upload to Zenodo"),console.log("   4. S3 public read       12. Publish DOI (irreversible)"),console.log("   5. Tag protection       13. S3 Object Lock"),console.log(F.sandbox?"   6. Create DOI (SANDBOX) 14. Generate archive":"   6. Create DOI           14. Generate archive"),console.log("   7. Update metadata      15. Notify user"),console.log("   8. Update README"),console.log(),F.sandbox)console.log(H.yellow("\u2501".repeat(60))),console.log(H.yellow.bold("                 SANDBOX MODE ENABLED")),console.log(H.yellow("\u2501".repeat(60))),console.log(H.yellow("  \u2022 DOI will be created in sandbox mode (EZID test shoulder)")),console.log(H.yellow("  \u2022 DOI will NOT be indexed by DataCite")),console.log(H.yellow("  \u2022 DOI will NOT resolve in production")),console.log(H.yellow("  \u2022 Use this for testing workflows only")),console.log(H.yellow("\u2501".repeat(60))),console.log();let J=await y0(`${$}?`,F);if(J!=="confirmed"){console.log(H.gray(J==="declined"?"Skipped":"Cancelled"));return}let Q=N("Running publication workflow (this may take a few minutes)...").start();try{let B=await bJ(D,!!F.resume,!!F.sandbox,!!F.skipCiCheck);if(Q.succeed(B.message),B.step_results&&B.step_results.length>0){console.log();let Y=B.step_results,X=Y.length;Y.forEach((G,W)=>{let q=`[${String(W+1).padStart(2," ")}/${X}]`,K=G.step.replace(/_/g," ");if(G.status==="completed"){let Z=(G.duration_ms/1000).toFixed(1),z=G.attempts>1?` (attempt ${G.attempts})`:"";console.log(`  ${H.green("[x]")} ${H.gray(q)} ${K} ${H.gray(`(${Z}s${z})`)}`)}else if(G.status==="failed")console.log(`  ${H.red("[!]")} ${H.gray(q)} ${K}${G.error?`: ${H.red(G.error)}`:""}`);else console.log(`  ${H.gray("[-]")} ${H.gray(q)} ${H.gray(K)} ${H.gray("(skipped)")}`)}),console.log()}else if(B.steps_completed){console.log();for(let Y of B.steps_completed)console.log(`  ${H.green("[x]")} ${Y.replace(/_/g," ")}`);console.log()}}catch(B){eD(B,Q,"Failed to approve publication",{422:"Fix the CI issues and retry with --resume"})}});KD.addCommand(dJ);KD.command("revert").description("Revert a dataset to a previous version (creates PR for review)").argument("<dataset-id>","Dataset ID (e.g., nm000104)").argument("[version]","Target version to revert to (e.g., 1.0.0)").option("--list","List available versions without reverting").option("--force","Direct push to main without PR (emergency only)").option("--message <msg>","Custom revert commit message").option("--dir <path>","Use existing local clone instead of cloning fresh").option(I0,S0).option(a0,g0).action(async(D,F,$)=>{if(!d0())return;let J=await A9();if(!J.allPassed){console.log(H.red("Error: Missing prerequisites"));for(let w of J.errors)console.log(H.gray(`  - ${w}`));return}let Q,B=!0;if($.dir){if(!mK0($.dir)){console.log(H.red(`Error: Directory not found: ${$.dir}`));return}Q=$.dir,B=!1}else Q=lK0(process.cwd(),`${D}-revert-${Date.now()}`);let Y=N("Fetching dataset info...").start(),X;try{X=await cD(D),Y.succeed(`Found dataset: ${X.name}`)}catch(w){if(w instanceof i){if(Y.fail(w.message),w.statusCode===404)console.log(H.gray("  Dataset not found"))}else Y.fail("Failed to fetch dataset");return}if(!X.github_repo){console.log(H.red("Error: Dataset has no GitHub repository"));return}if(B){let w=N(`Cloning ${D}...`).start(),I=`https://github.com/${X.github_repo}.git`,T=await U8(I,Q);if(!T.success){w.fail(`Clone failed: ${T.error}`);return}w.succeed(`Cloned to ${Q}`)}let G=await Hf(Q);if(G.length===0){console.log(H.yellow("No versions found for this dataset")),console.log(H.gray("  Dataset may not have any tagged releases yet"));return}if($.list){console.log(`
+`)),console.log("This will run the following 15-step orchestrator:"),console.log("   1. Check CI              9. Create version tag"),console.log("   2. Enrichment check     10. Create GitHub release"),console.log("   3. Make repo public     11. Upload to Zenodo"),console.log("   4. S3 public read       12. Publish DOI (irreversible)"),console.log("   5. Tag protection       13. S3 Object Lock"),console.log(F.sandbox?"   6. Create DOI (SANDBOX) 14. Generate archive":"   6. Create DOI           14. Generate archive"),console.log("   7. Update metadata      15. Notify user"),console.log("   8. Update README"),console.log(),F.sandbox)console.log(H.yellow("\u2501".repeat(60))),console.log(H.yellow.bold("                 SANDBOX MODE ENABLED")),console.log(H.yellow("\u2501".repeat(60))),console.log(H.yellow("  \u2022 DOI will be created in sandbox mode (EZID test shoulder)")),console.log(H.yellow("  \u2022 DOI will NOT be indexed by DataCite")),console.log(H.yellow("  \u2022 DOI will NOT resolve in production")),console.log(H.yellow("  \u2022 Use this for testing workflows only")),console.log(H.yellow("\u2501".repeat(60))),console.log();let J=await y0(`${$}?`,F);if(J!=="confirmed"){console.log(H.dim(J==="declined"?"Skipped":"Cancelled"));return}let Q=N("Running publication workflow (this may take a few minutes)...").start();try{let B=await bJ(D,!!F.resume,!!F.sandbox,!!F.skipCiCheck);if(Q.succeed(B.message),B.step_results&&B.step_results.length>0){console.log();let Y=B.step_results,X=Y.length;Y.forEach((G,W)=>{let q=`[${String(W+1).padStart(2," ")}/${X}]`,K=G.step.replace(/_/g," ");if(G.status==="completed"){let Z=(G.duration_ms/1000).toFixed(1),z=G.attempts>1?` (attempt ${G.attempts})`:"";console.log(`  ${H.green("[x]")} ${H.dim(q)} ${K} ${H.dim(`(${Z}s${z})`)}`)}else if(G.status==="failed")console.log(`  ${H.red("[!]")} ${H.dim(q)} ${K}${G.error?`: ${H.red(G.error)}`:""}`);else console.log(`  ${H.dim("[-]")} ${H.dim(q)} ${H.dim(K)} ${H.dim("(skipped)")}`)}),console.log()}else if(B.steps_completed){console.log();for(let Y of B.steps_completed)console.log(`  ${H.green("[x]")} ${Y.replace(/_/g," ")}`);console.log()}}catch(B){eD(B,Q,"Failed to approve publication",{422:"Fix the CI issues and retry with --resume"})}});KD.addCommand(dJ);KD.command("revert").description("Revert a dataset to a previous version (creates PR for review)").argument("<dataset-id>","Dataset ID (e.g., nm000104)").argument("[version]","Target version to revert to (e.g., 1.0.0)").option("--list","List available versions without reverting").option("--force","Direct push to main without PR (emergency only)").option("--message <msg>","Custom revert commit message").option("--dir <path>","Use existing local clone instead of cloning fresh").option(I0,S0).option(a0,g0).action(async(D,F,$)=>{if(!d0())return;let J=await A9();if(!J.allPassed){console.log(H.red("Error: Missing prerequisites"));for(let w of J.errors)console.log(H.dim(`  - ${w}`));return}let Q,B=!0;if($.dir){if(!mK0($.dir)){console.log(H.red(`Error: Directory not found: ${$.dir}`));return}Q=$.dir,B=!1}else Q=lK0(process.cwd(),`${D}-revert-${Date.now()}`);let Y=N("Fetching dataset info...").start(),X;try{X=await cD(D),Y.succeed(`Found dataset: ${X.name}`)}catch(w){if(w instanceof i){if(Y.fail(w.message),w.statusCode===404)console.log(H.dim("  Dataset not found"))}else Y.fail("Failed to fetch dataset");return}if(!X.github_repo){console.log(H.red("Error: Dataset has no GitHub repository"));return}if(B){let w=N(`Cloning ${D}...`).start(),I=`https://github.com/${X.github_repo}.git`,T=await U8(I,Q);if(!T.success){w.fail(`Clone failed: ${T.error}`);return}w.succeed(`Cloned to ${Q}`)}let G=await Hf(Q);if(G.length===0){console.log(H.yellow("No versions found for this dataset")),console.log(H.dim("  Dataset may not have any tagged releases yet"));return}if($.list){console.log(`
 ${H.cyan("Available Versions:")}
-`);for(let w of G)console.log(`  ${H.green(w.version)}  ${H.gray(w.date)}  ${H.gray(w.commit)}`);return}let W=F;if(!W){console.log(`
+`);for(let w of G)console.log(`  ${H.green(w.version)}  ${H.dim(w.date)}  ${H.dim(w.commit)}`);return}let W=F;if(!W){console.log(`
 ${H.cyan("Available Versions:")}
-`);for(let I of G)console.log(`  ${H.green(I.version)}  ${H.gray(I.date)}`);console.log();let{version:w}=await B0.prompt([{type:"list",name:"version",message:"Select version to revert to:",choices:G.map((I)=>({name:`${I.version} (${I.date})`,value:I.version}))}]);W=w}let q=await qf(Q,W);if(!q){console.log(H.red(`Error: Version ${W} not found`)),console.log(H.gray("  Use --list to see available versions"));return}if(console.log(),console.log(H.yellow("Revert Summary:")),console.log(`  Dataset:        ${H.cyan(D)}`),console.log(`  Target version: ${H.green(W)}`),console.log(`  Commit:         ${H.gray(q)}`),$.force)console.log(`  Mode:           ${H.red("DIRECT PUSH (--force)")}`);else console.log(`  Mode:           ${H.green("Pull Request")}`);if(console.log(),$.force)console.log(H.red("WARNING: --force will push directly to main without PR review!")),console.log(H.red("This should only be used in emergencies.")),console.log();let K=$.force?`Directly push revert to ${W}?`:`Create PR to revert to ${W}?`,Z=await y0(K,$);if(Z!=="confirmed"){console.log(H.gray(Z==="declined"?"Skipped":"Cancelled"));return}let z=`revert-to-${W.replace(/\./g,"-")}-${Date.now()}`,U=N("Creating revert branch...").start(),A=await Kf(Q,W,z);if(!A.success){U.fail(`Failed to create branch: ${A.error}`);return}U.succeed(`Created branch: ${z}`);let M=N("Committing revert...").start(),L=$.message||`Revert to version ${W}`,C=await Ef(Q,W,L);if(!C.success){M.fail(`Failed to commit: ${C.error}`);return}M.succeed("Committed revert changes");let O=N("Pushing branch...").start(),y=await L9(Q,z);if(!y.success){O.fail(`Failed to push: ${y.error}`);return}if(O.succeed("Pushed branch to GitHub"),!$.force){let w=N("Creating pull request...").start();try{let{spawn:I}=await import("child_process"),T=`Revert to version ${W}`,f=`## Revert Request
+`);for(let I of G)console.log(`  ${H.green(I.version)}  ${H.dim(I.date)}`);console.log();let{version:w}=await B0.prompt([{type:"list",name:"version",message:"Select version to revert to:",choices:G.map((I)=>({name:`${I.version} (${I.date})`,value:I.version}))}]);W=w}let q=await qf(Q,W);if(!q){console.log(H.red(`Error: Version ${W} not found`)),console.log(H.dim("  Use --list to see available versions"));return}if(console.log(),console.log(H.yellow("Revert Summary:")),console.log(`  Dataset:        ${H.cyan(D)}`),console.log(`  Target version: ${H.green(W)}`),console.log(`  Commit:         ${H.dim(q)}`),$.force)console.log(`  Mode:           ${H.red("DIRECT PUSH (--force)")}`);else console.log(`  Mode:           ${H.green("Pull Request")}`);if(console.log(),$.force)console.log(H.red("WARNING: --force will push directly to main without PR review!")),console.log(H.red("This should only be used in emergencies.")),console.log();let K=$.force?`Directly push revert to ${W}?`:`Create PR to revert to ${W}?`,Z=await y0(K,$);if(Z!=="confirmed"){console.log(H.dim(Z==="declined"?"Skipped":"Cancelled"));return}let z=`revert-to-${W.replace(/\./g,"-")}-${Date.now()}`,U=N("Creating revert branch...").start(),A=await Kf(Q,W,z);if(!A.success){U.fail(`Failed to create branch: ${A.error}`);return}U.succeed(`Created branch: ${z}`);let M=N("Committing revert...").start(),L=$.message||`Revert to version ${W}`,C=await Ef(Q,W,L);if(!C.success){M.fail(`Failed to commit: ${C.error}`);return}M.succeed("Committed revert changes");let O=N("Pushing branch...").start(),y=await L9(Q,z);if(!y.success){O.fail(`Failed to push: ${y.error}`);return}if(O.succeed("Pushed branch to GitHub"),!$.force){let w=N("Creating pull request...").start();try{let{spawn:I}=await import("child_process"),T=`Revert to version ${W}`,f=`## Revert Request
 This PR reverts the dataset to version ${W}.
 **Reason:** Admin-initiated revert
 **Target version:** ${W}
-**Original commit:** ${q}`,n=I("gh",["pr","create","--repo",X.github_repo,"--head",z,"--base","main","--title",T,"--body",f],{cwd:Q}),s="";n.stdout.on("data",(h)=>{s+=h.toString()}),await new Promise((h,t)=>{n.on("close",(t0)=>{if(t0===0)h();else t(Error(`gh pr create failed with code ${t0}`))})}),w.succeed("Created pull request"),console.log(),console.log(`  ${H.cyan("PR URL:")} ${s.trim()}`),console.log(),console.log(H.green("Revert PR created successfully.")),console.log(H.gray("The PR will go through validation checks before it can be merged."))}catch(I){w.fail("Failed to create PR via gh CLI");let T=I instanceof Error?I.message:String(I);if(console.error(H.red(`  Error: ${T}`)),T.includes("not found")||T.includes("command not found"))console.log(H.yellow("  Possible causes:")),console.log("    \u2022 GitHub CLI (gh) not installed or not in PATH"),console.log("    \u2022 Run: brew install gh  (or see https://cli.github.com)");else if(T.includes("auth")||T.includes("401"))console.log(H.yellow("  GitHub authentication failed.")),console.log("    \u2022 Run: gh auth login");console.log(H.gray("  You may need to create the PR manually on GitHub")),console.log(H.gray(`  Branch: ${z}`))}}else console.log(H.yellow("Force mode: Merging directly to main...")),console.log(H.red("Direct merge not implemented for safety.")),console.log(H.gray("To force-merge, manually merge the branch on GitHub:")),console.log(H.gray(`  git checkout main && git merge ${z} && git push`));if(B)console.log(),console.log(H.gray(`Working directory: ${Q}`)),console.log(H.gray("You can delete this directory after the PR is merged."))});KD.command("make-public").description("Publish a dataset (make repository and data public) - PERMANENT").argument("<dataset-id>","Dataset ID (e.g., nm000104)").addHelpText("after",`
+**Original commit:** ${q}`,n=I("gh",["pr","create","--repo",X.github_repo,"--head",z,"--base","main","--title",T,"--body",f],{cwd:Q}),s="";n.stdout.on("data",(h)=>{s+=h.toString()}),await new Promise((h,t)=>{n.on("close",(t0)=>{if(t0===0)h();else t(Error(`gh pr create failed with code ${t0}`))})}),w.succeed("Created pull request"),console.log(),console.log(`  ${H.cyan("PR URL:")} ${s.trim()}`),console.log(),console.log(H.green("Revert PR created successfully.")),console.log(H.dim("The PR will go through validation checks before it can be merged."))}catch(I){w.fail("Failed to create PR via gh CLI");let T=I instanceof Error?I.message:String(I);if(console.error(H.red(`  Error: ${T}`)),T.includes("not found")||T.includes("command not found"))console.log(H.yellow("  Possible causes:")),console.log("    \u2022 GitHub CLI (gh) not installed or not in PATH"),console.log("    \u2022 Run: brew install gh  (or see https://cli.github.com)");else if(T.includes("auth")||T.includes("401"))console.log(H.yellow("  GitHub authentication failed.")),console.log("    \u2022 Run: gh auth login");console.log(H.dim("  You may need to create the PR manually on GitHub")),console.log(H.dim(`  Branch: ${z}`))}}else console.log(H.yellow("Force mode: Merging directly to main...")),console.log(H.red("Direct merge not implemented for safety.")),console.log(H.dim("To force-merge, manually merge the branch on GitHub:")),console.log(H.dim(`  git checkout main && git merge ${z} && git push`));if(B)console.log(),console.log(H.dim(`Working directory: ${Q}`)),console.log(H.dim("You can delete this directory after the PR is merged."))});KD.command("make-public").description("Publish a dataset (make repository and data public) - PERMANENT").argument("<dataset-id>","Dataset ID (e.g., nm000104)").addHelpText("after",`
 Description:
   Publish a dataset by making both the GitHub repository and S3 data publicly accessible.
@@ -315,13 +315,13 @@ Examples:
 `).action(async(D)=>{if(!d0())return;let F=D.trim(),$;try{$=await cD(F)}catch(B){if(B instanceof i&&B.statusCode===404)console.error(H.red(`Dataset '${F}' not found`));else console.error(H.red(`Failed to fetch dataset: ${B instanceof Error?B.message:String(B)}`));process.exit(1)}if(console.log(H.yellow(`
 WARNING: Publishing is PERMANENT and IRREVERSIBLE
 `)),console.log("This will:"),console.log("  1. Make the GitHub repository PUBLIC"),console.log("  2. Allow public S3 access to all dataset files"),console.log(`  3. Update git-annex configuration for web access
-`),console.log(`Dataset: ${H.cyan($.dataset_id)} - ${$.name}`),$.owner_username)console.log(`Owner: ${$.owner_username}`);if($.github_repo)console.log(`Repository: ${$.github_repo}`);if(console.log(),(await B0.prompt([{type:"input",name:"datasetId",message:`Type '${F}' to confirm:`,validate:(B)=>{if(B.trim()===F)return!0;return`Please type exactly '${F}' to confirm`}}])).datasetId!==F)console.log(H.gray("Cancelled.")),process.exit(0);let Q=N("Publishing dataset...").start();try{let B=await R_(F);Q.succeed(H.green("Dataset published successfully")),console.log(`
+`),console.log(`Dataset: ${H.cyan($.dataset_id)} - ${$.name}`),$.owner_username)console.log(`Owner: ${$.owner_username}`);if($.github_repo)console.log(`Repository: ${$.github_repo}`);if(console.log(),(await B0.prompt([{type:"input",name:"datasetId",message:`Type '${F}' to confirm:`,validate:(B)=>{if(B.trim()===F)return!0;return`Please type exactly '${F}' to confirm`}}])).datasetId!==F)console.log(H.dim("Cancelled.")),process.exit(0);let Q=N("Publishing dataset...").start();try{let B=await R_(F);Q.succeed(H.green("Dataset published successfully")),console.log(`
 GitHub: ${H.cyan(B.github_url)}`),console.log(`S3: ${H.cyan(B.s3_url)}`)}catch(B){if(Q.fail(H.red("Failed to publish dataset")),B instanceof i){if(console.error(H.red(`
-${B.message}`)),B.details)console.error(H.gray(JSON.stringify(B.details,null,2)));if(B.statusCode===403)console.log(H.gray("  You must be the dataset owner or an admin to publish"));else if(B.statusCode===400&&B.message.includes("sandbox"))console.log(H.gray("  Sandbox datasets cannot be published"))}else console.error(H.red(`
+${B.message}`)),B.details)console.error(H.dim(JSON.stringify(B.details,null,2)));if(B.statusCode===403)console.log(H.dim("  You must be the dataset owner or an admin to publish"));else if(B.statusCode===400&&B.message.includes("sandbox"))console.log(H.dim("  Sandbox datasets cannot be published"))}else console.error(H.red(`
 ${B instanceof Error?B.message:String(B)}`));process.exit(1)}});KD.command("delete-dataset").description("Delete a dataset and all associated resources (GitHub, S3, D1)").argument("<dataset-id>","Dataset ID (e.g., nm000108)").option("--force","Force deletion of published datasets with DOIs (owner only)").action(async(D,F)=>{if(!d0())return;let $=N("Looking up dataset...").start();try{let J=await cD(D);if($.stop(),console.log(H.bold(`
 Dataset: ${J.dataset_id}`)),console.log(`  Name: ${J.name||"(unnamed)"}`),console.log(`  Visibility: ${J.visibility}`),J.concept_doi){if(console.log(`  DOI: ${J.concept_doi}`),console.log(H.yellow(`
-  WARNING: This dataset has a DOI. Only the NEMAR owner can delete it.`)),!F.force)console.log(H.gray("  Use --force to confirm deletion of published datasets.")),process.exit(1)}let{proceed:Q}=await B0.prompt([{type:"confirm",name:"proceed",message:H.red(`Delete dataset ${D}? This will remove the GitHub repo, S3 data, and all database records. This cannot be undone.`),default:!1}]);if(!Q){console.log(H.gray("Cancelled."));return}$.start("Deleting dataset...");let B=await n_(D,F.force??!1);if(!B.deleted)$.fail("Dataset deletion incomplete");else if(B.warnings.length>0)$.warn("Dataset deleted with warnings");else $.succeed("Dataset deleted");if(console.log(H.bold(`
-Deletion summary:`)),console.log(`  GitHub repo: ${B.steps.github.success?H.green("deleted"):H.red("failed")}`),B.steps.s3.skipped)console.log(`  S3 objects: ${H.yellow("skipped (published dataset)")}`);else{let Y=H.green(`${B.steps.s3.deleted} deleted`);if(B.steps.s3.failed.length>0)Y+=H.red(`, ${B.steps.s3.failed.length} failed`);console.log(`  S3 objects: ${Y}`)}if(console.log(`  Database: ${B.steps.d1.success?H.green("cleaned up"):H.red("failed")}`),B.steps.d1.versionsDeleted>0)console.log(H.gray(`    ${B.steps.d1.versionsDeleted} version records removed`));if(B.steps.d1.pubRequestsDeleted>0)console.log(H.gray(`    ${B.steps.d1.pubRequestsDeleted} publication requests removed`));if(B.warnings.length>0){console.log(H.yellow(`
+  WARNING: This dataset has a DOI. Only the NEMAR owner can delete it.`)),!F.force)console.log(H.dim("  Use --force to confirm deletion of published datasets.")),process.exit(1)}let{proceed:Q}=await B0.prompt([{type:"confirm",name:"proceed",message:H.red(`Delete dataset ${D}? This will remove the GitHub repo, S3 data, and all database records. This cannot be undone.`),default:!1}]);if(!Q){console.log(H.dim("Cancelled."));return}$.start("Deleting dataset...");let B=await n_(D,F.force??!1);if(!B.deleted)$.fail("Dataset deletion incomplete");else if(B.warnings.length>0)$.warn("Dataset deleted with warnings");else $.succeed("Dataset deleted");if(console.log(H.bold(`
+Deletion summary:`)),console.log(`  GitHub repo: ${B.steps.github.success?H.green("deleted"):H.red("failed")}`),B.steps.s3.skipped)console.log(`  S3 objects: ${H.yellow("skipped (published dataset)")}`);else{let Y=H.green(`${B.steps.s3.deleted} deleted`);if(B.steps.s3.failed.length>0)Y+=H.red(`, ${B.steps.s3.failed.length} failed`);console.log(`  S3 objects: ${Y}`)}if(console.log(`  Database: ${B.steps.d1.success?H.green("cleaned up"):H.red("failed")}`),B.steps.d1.versionsDeleted>0)console.log(H.dim(`    ${B.steps.d1.versionsDeleted} version records removed`));if(B.steps.d1.pubRequestsDeleted>0)console.log(H.dim(`    ${B.steps.d1.pubRequestsDeleted} publication requests removed`));if(B.warnings.length>0){console.log(H.yellow(`
 Warnings:`));for(let Y of B.warnings)console.log(H.yellow(`  - ${Y}`))}}catch(J){eD(J,$,"Failed to delete dataset",{403:"Published datasets can only be deleted by the NEMAR owner",404:"Dataset not found",409:"Cannot delete dataset with active publication requests"}),process.exit(1)}});KD.command("import-openneuro").description("Import an OpenNeuro dataset into NEMAR").argument("<openneuro-id>","OpenNeuro dataset ID (e.g., ds007262)").option("--dir <path>","Working directory for clone (default: temp dir)").option("--skip-data","Skip S3 data copy (metadata only)").action(async(D,F)=>{if(!d0())return;let{importOpenNeuro:$}=await Promise.resolve().then(() => (Rf(),Cf));try{await $(D,{workDir:F.dir,skipData:F.skipData})}catch(J){let Q=J instanceof Error?J.message:String(J);console.error(H.red(`
 Import failed: ${Q}`)),process.exit(1)}});KD.command("e2e-test").description("Run end-to-end test against nm099999 (admin only)").option("--verbose","Show detailed output for each step").option("--skip-reset","Use existing nm099999 state (skip reset)").option("--skip-cleanup","Keep temp directories after test").addHelpText("after",`
 Description:
@@ -338,7 +338,7 @@ Steps:
 Requirements:
   - Admin privileges (API role check)
   - git-annex installed
-  - GitHub SSH or gh CLI configured
+  - GitHub CLI authenticated (gh auth login)
   - Active nemar auth session
 Examples:
@@ -347,11 +347,11 @@ Examples:
   $ nemar admin e2e-test --skip-cleanup     # Keep temp dirs for inspection
   $ nemar admin e2e-test --skip-reset       # Reuse existing nm099999 state`).action(async(D)=>{if(!d0())return;console.log(H.cyan(`
 NEMAR E2E Test (nm099999)
-`));let{runE2ETest:F}=await Promise.resolve().then(() => (kf(),Sf)),$=await F({verbose:D.verbose,skipReset:D.skipReset,skipCleanup:D.skipCleanup});console.log();for(let Q of $.steps){let B=Q.passed?H.green("[x]"):H.red("[ ]"),Y=H.gray(`(${Q.duration_ms}ms)`);if(console.log(`  ${B} ${Q.name} ${Y}`),Q.error)console.log(H.red(`      ${Q.error}`))}console.log();let J=($.total_duration_ms/1000).toFixed(1);if($.passed)console.log(H.green(`All ${$.steps.length} steps passed (${J}s)`));else{let Q=$.steps.filter((B)=>!B.passed).length;console.log(H.red(`${Q}/${$.steps.length} steps failed (${J}s)`))}if($.upload_dir)console.log(H.gray(`
-Upload dir: ${$.upload_dir}`)),console.log(H.gray(`Clone dir:  ${$.clone_dir}`));process.exit($.passed?0:1)});var HW=new FD("sync").description("Sync dataset metadata to nemar.org datapipeline");HW.command("run").description("Sync a dataset to nemar.org").argument("<dataset-id>","Dataset ID (e.g., nm000103)").action(async(D)=>{if(!d0())return;let F=N(`Syncing ${D} to nemar.org...`).start();try{let $=await a_(D);if($.synced)F.succeed(`${D} synced to nemar.org`);else{F.warn(`${D} sync completed with errors:`);for(let J of $.errors)console.log(H.red(`  - ${J}`))}}catch($){F.fail(`Failed to sync ${D}`),console.error(H.red(p0($)))}});HW.command("status").description("Show nemar.org sync status for all published datasets").action(async()=>{if(!d0())return;let D=N("Fetching sync status...").start();try{let F=await o_();if(D.stop(),console.log(H.bold(`
+`));let{runE2ETest:F}=await Promise.resolve().then(() => (kf(),Sf)),$=await F({verbose:D.verbose,skipReset:D.skipReset,skipCleanup:D.skipCleanup});console.log();for(let Q of $.steps){let B=Q.passed?H.green("[x]"):H.red("[ ]"),Y=H.dim(`(${Q.duration_ms}ms)`);if(console.log(`  ${B} ${Q.name} ${Y}`),Q.error)console.log(H.red(`      ${Q.error}`))}console.log();let J=($.total_duration_ms/1000).toFixed(1);if($.passed)console.log(H.green(`All ${$.steps.length} steps passed (${J}s)`));else{let Q=$.steps.filter((B)=>!B.passed).length;console.log(H.red(`${Q}/${$.steps.length} steps failed (${J}s)`))}if($.upload_dir)console.log(H.dim(`
+Upload dir: ${$.upload_dir}`)),console.log(H.dim(`Clone dir:  ${$.clone_dir}`));process.exit($.passed?0:1)});var HW=new FD("sync").description("Sync dataset metadata to nemar.org datapipeline");HW.command("run").description("Sync a dataset to nemar.org").argument("<dataset-id>","Dataset ID (e.g., nm000103)").action(async(D)=>{if(!d0())return;let F=N(`Syncing ${D} to nemar.org...`).start();try{let $=await a_(D);if($.synced)F.succeed(`${D} synced to nemar.org`);else{F.warn(`${D} sync completed with errors:`);for(let J of $.errors)console.log(H.red(`  - ${J}`))}}catch($){F.fail(`Failed to sync ${D}`),console.error(H.red(p0($)))}});HW.command("status").description("Show nemar.org sync status for all published datasets").action(async()=>{if(!d0())return;let D=N("Fetching sync status...").start();try{let F=await o_();if(D.stop(),console.log(H.bold(`
 nemar.org Sync Status (${F.total} datasets)
 `)),console.log(`  Synced: ${H.green(F.synced)}  Failed: ${H.red(F.failed)}  Pending: ${H.yellow(F.pending)}
-`),F.datasets.length===0){console.log(H.gray("  No published datasets found."));return}console.log(H.gray(`  ${"ID".padEnd(12)} ${"Name".padEnd(40)} ${"Status".padEnd(10)} ${"Last Sync".padEnd(20)}`)),console.log(H.gray(`  ${"\u2500".repeat(85)}`));for(let $ of F.datasets){let J=$.nemar_sync_status||"pending",Q=J==="synced"?H.green:J==="failed"?H.red:H.yellow,B=$.nemar_sync_at?new Date($.nemar_sync_at).toLocaleDateString():"-",Y=$.name||$.dataset_id,X=Y.length>38?`${Y.substring(0,35)}...`:Y;if(console.log(`  ${$.dataset_id.padEnd(12)} ${X.padEnd(40)} ${Q(J.padEnd(10))} ${B}`),$.nemar_sync_error)console.log(H.red(`    Error: ${$.nemar_sync_error}`))}}catch(F){D.fail("Failed to fetch sync status"),console.error(H.red(p0(F)))}});KD.addCommand(HW);N1();N6();v3();O4();KF();import{appendFileSync as pK0,existsSync as b6,mkdirSync as xf,readFileSync as nJ,writeFileSync as dK0}from"fs";import{homedir as cK0}from"os";import{join as cJ}from"path";var{spawn:_f}=globalThis.Bun;function I4(){let D=cJ(cK0(),".ssh");return{sshDir:D,privateKey:cJ(D,"nemar_ed25519"),publicKey:cJ(D,"nemar_ed25519.pub"),configFile:cJ(D,"config")}}function ff(){let D=I4();return b6(D.privateKey)&&b6(D.publicKey)}async function gf(D){let F=I4();if(!b6(F.sshDir))try{xf(F.sshDir,{mode:448})}catch($){return{success:!1,error:`Cannot create ~/.ssh directory: ${$.message}`}}if(b6(F.privateKey))try{return{success:!0,publicKey:nJ(F.publicKey,"utf-8").trim()}}catch($){return{success:!1,error:`NEMAR SSH key exists but cannot read public key: ${$.message}`}}try{let $=_f({cmd:["ssh-keygen","-t","ed25519","-f",F.privateKey,"-N","","-C",`nemar-cli-${D}`],stdout:"pipe",stderr:"pipe"}),J=await new Response($.stderr).text();if(await $.exited!==0)return{success:!1,error:`ssh-keygen failed: ${J}`};return{success:!0,publicKey:nJ(F.publicKey,"utf-8").trim()}}catch($){return{success:!1,error:`Failed to generate SSH key: ${$.message}`}}}function hf(){let D=I4();if(!b6(D.publicKey))return null;try{return nJ(D.publicKey,"utf-8").trim()}catch{return null}}function nK0(){let D=I4();if(!b6(D.configFile))return!1;try{let F=nJ(D.configFile,"utf-8");return F.includes("IdentityFile ~/.ssh/nemar_ed25519")||F.includes(`IdentityFile ${D.privateKey}`)}catch{return!1}}function bf(){let D=I4();if(!b6(D.sshDir))try{xf(D.sshDir,{mode:448})}catch($){return{success:!1,error:`Cannot create ~/.ssh directory: ${$.message}`}}if(nK0())return{success:!0};let F=`
+`),F.datasets.length===0){console.log(H.dim("  No published datasets found."));return}console.log(H.dim(`  ${"ID".padEnd(12)} ${"Name".padEnd(40)} ${"Status".padEnd(10)} ${"Last Sync".padEnd(20)}`)),console.log(H.dim(`  ${"\u2500".repeat(85)}`));for(let $ of F.datasets){let J=$.nemar_sync_status||"pending",Q=J==="synced"?H.green:J==="failed"?H.red:H.yellow,B=$.nemar_sync_at?new Date($.nemar_sync_at).toLocaleDateString():"-",Y=$.name||$.dataset_id,X=Y.length>38?`${Y.substring(0,35)}...`:Y;if(console.log(`  ${$.dataset_id.padEnd(12)} ${X.padEnd(40)} ${Q(J.padEnd(10))} ${B}`),$.nemar_sync_error)console.log(H.red(`    Error: ${$.nemar_sync_error}`))}}catch(F){D.fail("Failed to fetch sync status"),console.error(H.red(p0(F)))}});KD.addCommand(HW);N1();N6();v3();O4();KF();import{appendFileSync as pK0,existsSync as b6,mkdirSync as xf,readFileSync as nJ,writeFileSync as dK0}from"fs";import{homedir as cK0}from"os";import{join as cJ}from"path";var{spawn:_f}=globalThis.Bun;function I4(){let D=cJ(cK0(),".ssh");return{sshDir:D,privateKey:cJ(D,"nemar_ed25519"),publicKey:cJ(D,"nemar_ed25519.pub"),configFile:cJ(D,"config")}}function ff(){let D=I4();return b6(D.privateKey)&&b6(D.publicKey)}async function gf(D){let F=I4();if(!b6(F.sshDir))try{xf(F.sshDir,{mode:448})}catch($){return{success:!1,error:`Cannot create ~/.ssh directory: ${$.message}`}}if(b6(F.privateKey))try{return{success:!0,publicKey:nJ(F.publicKey,"utf-8").trim()}}catch($){return{success:!1,error:`NEMAR SSH key exists but cannot read public key: ${$.message}`}}try{let $=_f({cmd:["ssh-keygen","-t","ed25519","-f",F.privateKey,"-N","","-C",`nemar-cli-${D}`],stdout:"pipe",stderr:"pipe"}),J=await new Response($.stderr).text();if(await $.exited!==0)return{success:!1,error:`ssh-keygen failed: ${J}`};return{success:!0,publicKey:nJ(F.publicKey,"utf-8").trim()}}catch($){return{success:!1,error:`Failed to generate SSH key: ${$.message}`}}}function hf(){let D=I4();if(!b6(D.publicKey))return null;try{return nJ(D.publicKey,"utf-8").trim()}catch{return null}}function nK0(){let D=I4();if(!b6(D.configFile))return!1;try{let F=nJ(D.configFile,"utf-8");return F.includes("IdentityFile ~/.ssh/nemar_ed25519")||F.includes(`IdentityFile ${D.privateKey}`)}catch{return!1}}function bf(){let D=I4();if(!b6(D.sshDir))try{xf(D.sshDir,{mode:448})}catch($){return{success:!1,error:`Cannot create ~/.ssh directory: ${$.message}`}}if(nK0())return{success:!0};let F=`
 # NEMAR CLI SSH key (auto-generated)
 Host github.com
   AddKeysToAgent yes
@@ -380,15 +380,15 @@ Examples:
   $ nemar auth whoami                    # Alias for status
   $ nemar auth switch                    # Switch between accounts
   $ nemar auth logout                    # Clear active account
-  $ nemar auth logout --all              # Clear all accounts`);async function KW(D){if(v0()){let J=YD();if(console.log(H.yellow(`Already logged in as ${J.username||"unknown"}`)),console.log(H.gray("  This will add another account (use 'nemar auth switch' to switch)")),await y0("Log in with a different account?",D)!=="confirmed")return}let F=D.key||process.env.NEMAR_API_KEY;if(!F)F=(await B0.prompt([{type:"password",name:"apiKey",message:"Enter your API key:",mask:"*",validate:(Q)=>{if(!Q||Q.length<32)return"Please enter a valid API key";return!0}}])).apiKey;if(!F){console.log(H.red("No API key provided"));return}let $=N("Validating API key...").start();try{let J=await z_(F);if(!J.valid){$.fail("Invalid API key");return}if(Y_(J.user.username,{apiKey:F,apiUrl:"https://nemar-api-dev.shirazi-10f.workers.dev",username:J.user.username,email:J.user.email,githubUsername:J.user.github_username,sandboxCompleted:J.user.sandbox_completed,...J.user.sandbox_dataset_id?{sandboxDatasetId:J.user.sandbox_dataset_id}:{}}),$.succeed("Login successful"),console.log(),console.log(`  Welcome back, ${H.cyan(J.user.username)}!`),J.user.role==="owner")console.log(`  ${H.red("Owner access enabled")}`);else if(J.user.role==="admin")console.log(`  ${H.magenta("Admin access enabled")}`);if(!J.user.sandbox_completed)console.log(),console.log(H.yellow("  Note: Sandbox training required before uploading datasets")),console.log(H.gray("  Run 'nemar sandbox' to complete training"))}catch(J){if(J instanceof i){if($.fail(J.message),J.statusCode===401)console.log(H.gray("  Check that your API key is correct"));else if(J.statusCode===403)console.log(H.gray("  Your account may not be approved yet"))}else $.fail("Connection failed"),console.log(H.gray("  Check your internet connection"))}}var iK0=D1.command("login").description("Authenticate with your NEMAR API key").option("-k, --key <key>","API key (alternative: set NEMAR_API_KEY env var)").option(I0,S0).option(a0,g0).action(KW);m6(iK0,`
+  $ nemar auth logout --all              # Clear all accounts`);async function KW(D){if(v0()){let J=YD();if(console.log(H.yellow(`Already logged in as ${J.username||"unknown"}`)),console.log(H.dim("  This will add another account (use 'nemar auth switch' to switch)")),await y0("Log in with a different account?",D)!=="confirmed")return}let F=D.key||process.env.NEMAR_API_KEY;if(!F)F=(await B0.prompt([{type:"password",name:"apiKey",message:"Enter your API key:",mask:"*",validate:(Q)=>{if(!Q||Q.length<32)return"Please enter a valid API key";return!0}}])).apiKey;if(!F){console.log(H.red("No API key provided"));return}let $=N("Validating API key...").start();try{let J=await z_(F);if(!J.valid){$.fail("Invalid API key");return}if(Y_(J.user.username,{apiKey:F,apiUrl:"https://nemar-api-dev.shirazi-10f.workers.dev",username:J.user.username,email:J.user.email,githubUsername:J.user.github_username,sandboxCompleted:J.user.sandbox_completed,...J.user.sandbox_dataset_id?{sandboxDatasetId:J.user.sandbox_dataset_id}:{}}),$.succeed("Login successful"),console.log(),console.log(`  Welcome back, ${H.cyan(J.user.username)}!`),J.user.role==="owner")console.log(`  ${H.red("Owner access enabled")}`);else if(J.user.role==="admin")console.log(`  ${H.magenta("Admin access enabled")}`);if(!J.user.sandbox_completed)console.log(),console.log(H.yellow("  Note: Sandbox training required before uploading datasets")),console.log(H.dim("  Run 'nemar sandbox' to complete training"))}catch(J){if(J instanceof i){if($.fail(J.message),J.statusCode===401)console.log(H.dim("  Check that your API key is correct"));else if(J.statusCode===403)console.log(H.dim("  Your account may not be approved yet"))}else $.fail("Connection failed"),console.log(H.dim("  Check your internet connection"))}}var iK0=D1.command("login").description("Authenticate with your NEMAR API key").option("-k, --key <key>","API key (alternative: set NEMAR_API_KEY env var)").option(I0,S0).option(a0,g0).action(KW);m6(iK0,`
 Environment Variables:
   NEMAR_API_KEY    Your API key (alternative to -k flag)
 Examples:
   $ nemar auth login                     # Interactive prompt
   $ nemar auth login -k nemar_abc123...  # Provide key directly
-  $ NEMAR_API_KEY=nemar_abc... nemar auth login`);async function iJ(){console.log(H.cyan("NEMAR Account Registration")),console.log(H.gray(`Create an account to upload and manage datasets
-`));let D=await B0.prompt([{type:"input",name:"username",message:"Choose a username:",validate:async($)=>{if(!$||$.length<3)return"Username must be at least 3 characters";if($.length>30)return"Username must be at most 30 characters";if(!/^[a-zA-Z0-9_-]+$/.test($))return"Username can only contain letters, numbers, underscores, and hyphens";try{let J=await q_($);if(!J.available)return J.reason||`Username "${$}" is already taken`}catch(J){if(J instanceof i&&J.statusCode===0)return!0;return!0}return!0}},{type:"input",name:"email",message:"Email address:",validate:($)=>{if(!$||!/^[^\s@]+@[^\s@]+\.[^\s@]+$/.test($))return"Please enter a valid email address";return!0}},{type:"password",name:"password",message:"Password (min 12 characters):",mask:"*",validate:($)=>{if(!$||$.length<12)return"Password must be at least 12 characters";if($.length>128)return"Password must be at most 128 characters";return!0}},{type:"password",name:"confirmPassword",message:"Confirm password:",mask:"*",validate:($,J)=>{if($!==J?.password)return"Passwords do not match";return!0}},{type:"input",name:"github_username",message:"GitHub username (for PR collaboration):",validate:async($)=>{if(!$||$.length<1)return"GitHub username is required for PR collaboration";if($.length>39)return"GitHub username is too long";try{if(!(await K_($)).valid)return`GitHub user "${$}" not found. Please check the username.`}catch(J){if(J instanceof i&&J.statusCode===0)return!0;return!0}return!0}},{type:"input",name:"orcid",message:"ORCID iD (optional, e.g. 0000-0002-1825-0097):",validate:($)=>{if(!$||$.trim()==="")return!0;if(!/^\d{4}-\d{4}-\d{4}-\d{3}[\dX]$/.test($.trim()))return"ORCID must be in format 0000-0000-0000-000X";return!0}},{type:"input",name:"description",message:"Why do you need access to NEMAR? (1-2 sentences):",validate:($)=>{let J=$?.trim();if(!J||J.length<20)return"Please provide at least 20 characters describing why you need NEMAR access";if(J.length>500)return"Description must be at most 500 characters";return!0}}]),F=N("Creating account...").start();try{let $=await E_({username:D.username,email:D.email,password:D.password,github_username:D.github_username,description:D.description.trim(),orcid:D.orcid?.trim()||void 0});F.succeed("Account created"),console.log(),console.log(H.green("Registration successful!")),console.log(),console.log("Next steps:"),$.next_steps.forEach((J,Q)=>{console.log(`  ${Q+1}. ${J}`)}),console.log(),console.log(H.gray("Once approved, use 'nemar auth retrieve-key' to get your API key"))}catch($){if($ instanceof i){if(F.fail($.message),$.details&&Array.isArray($.details))$.details.forEach((J)=>{console.log(H.gray(`  - ${J}`))});if($.message.includes("already taken"))console.log(H.gray("  Try a different username"));else if($.message.includes("already registered"))console.log(H.gray("  Use 'nemar auth resend-verification' if you need a new verification link"))}else F.fail("Registration failed"),console.log(H.gray(`  ${$ instanceof Error?$.message:"Unknown error"}`))}}D1.command("signup").description("Register for a new NEMAR account").action(iJ);async function aJ(D){if(!v0()){console.log(H.yellow("Not authenticated")),console.log(),console.log("  Run 'nemar auth login' to authenticate"),console.log("  Run 'nemar auth signup' to create an account");return}let F;if(D.refresh){let B=N("Fetching user info...").start();try{let Y=await xJ();l8("username",Y.username),l8("email",Y.email),l8("githubUsername",Y.github_username),F=Y.role,B.stop()}catch(Y){if(B.fail("Could not refresh user info"),Y instanceof i&&Y.statusCode===401)console.log(H.gray("  Your session may have expired. Try logging in again."))}}let $=YD();if(console.log(H.green("Authenticated")),console.log(),$.username)console.log(`  Username: ${H.cyan($.username)}`);if($.email)console.log(`  Email:    ${$.email}`);if($.githubUsername)console.log(`  GitHub:   @${$.githubUsername}`);if(F){let B=F==="owner"?H.red("Owner"):F==="admin"?H.magenta("Admin"):H.white("Member");console.log(`  Role:     ${B}`)}console.log(`  Config:   ${H.gray(B_())}`);let Q=V9().filter((B)=>!B.active);if(Q.length>0)console.log(),console.log(`  Other accounts: ${Q.map((B)=>H.gray(B.username)).join(", ")}`),console.log(H.gray("  Run 'nemar auth switch' to switch accounts"))}D1.command("status").description("Check current authentication status").option("--refresh","Refresh user info from server").action(aJ);D1.command("whoami").description("Show current user (alias for status)").option("--refresh","Refresh user info from server").action(aJ);async function aK0(D){try{let F=Bun.which("gh");if(!F){console.log(H.gray("  GitHub CLI (gh) not found in PATH, skipping"));return}let $=Bun.spawn({cmd:[F,"auth","switch","--user",D],stdout:"pipe",stderr:"pipe"}),J=await new Response($.stderr).text(),Q=await $.exited;if(Q===0)console.log(`  GitHub CLI switched to ${H.cyan(`@${D}`)}`);else{let B=J.trim();if(B.includes("not found")||B.includes("no accounts"))console.log(H.gray(`  GitHub CLI: @${D} not logged in (run 'gh auth login')`));else console.log(H.gray(`  GitHub CLI switch failed: ${B||`exit code ${Q}`}`))}}catch(F){let $=F instanceof Error?F.message:String(F);console.log(H.gray(`  GitHub CLI switch skipped: ${$}`))}}async function EW(D){let F=V9();if(F.length===0){console.log(H.yellow("No stored accounts")),console.log("  Run 'nemar auth login' to add an account");return}if(F.length===1){let B=F[0];if(B.active){console.log(H.yellow(`Only one account stored: ${B.username}`)),console.log("  Run 'nemar auth login' to add another account");return}}let $;if(D)$=D;else{let B=F.map((X)=>({name:`${X.username}${X.githubUsername?` (@${X.githubUsername})`:""}${X.active?H.green(" (active)"):""}`,value:X.username,short:X.username})),{selected:Y}=await B0.prompt([{type:"list",name:"selected",message:"Switch to account:",choices:B,default:F.find((X)=>X.active)?.username}]);$=Y}let J=F.find((B)=>B.active);if(J&&J.username===$){console.log(H.yellow(`Already using account ${$}`));return}let Q=X_($);if(!Q){console.log(H.red(`Account not found: ${$}`)),console.log(H.gray("  Provide a NEMAR username or GitHub username")),console.log(H.gray(`  Available: ${F.map((B)=>B.username).join(", ")}`));return}if(console.log(H.green(`Switched to ${H.cyan(Q.username||$)}`)),Q.githubUsername)await aK0(Q.githubUsername)}var oK0=D1.command("switch [username]").description("Switch between stored accounts").action(EW);m6(oK0,`
+  $ NEMAR_API_KEY=nemar_abc... nemar auth login`);async function iJ(){console.log(H.cyan("NEMAR Account Registration")),console.log(H.dim(`Create an account to upload and manage datasets
+`));let D=await B0.prompt([{type:"input",name:"username",message:"Choose a username:",validate:async($)=>{if(!$||$.length<3)return"Username must be at least 3 characters";if($.length>30)return"Username must be at most 30 characters";if(!/^[a-zA-Z0-9_-]+$/.test($))return"Username can only contain letters, numbers, underscores, and hyphens";try{let J=await q_($);if(!J.available)return J.reason||`Username "${$}" is already taken`}catch(J){if(J instanceof i&&J.statusCode===0)return!0;return!0}return!0}},{type:"input",name:"email",message:"Email address:",validate:($)=>{if(!$||!/^[^\s@]+@[^\s@]+\.[^\s@]+$/.test($))return"Please enter a valid email address";return!0}},{type:"password",name:"password",message:"Password (min 12 characters):",mask:"*",validate:($)=>{if(!$||$.length<12)return"Password must be at least 12 characters";if($.length>128)return"Password must be at most 128 characters";return!0}},{type:"password",name:"confirmPassword",message:"Confirm password:",mask:"*",validate:($,J)=>{if($!==J?.password)return"Passwords do not match";return!0}},{type:"input",name:"github_username",message:"GitHub username (for PR collaboration):",validate:async($)=>{if(!$||$.length<1)return"GitHub username is required for PR collaboration";if($.length>39)return"GitHub username is too long";try{if(!(await K_($)).valid)return`GitHub user "${$}" not found. Please check the username.`}catch(J){if(J instanceof i&&J.statusCode===0)return!0;return!0}return!0}},{type:"input",name:"orcid",message:"ORCID iD (optional, e.g. 0000-0002-1825-0097):",validate:($)=>{if(!$||$.trim()==="")return!0;if(!/^\d{4}-\d{4}-\d{4}-\d{3}[\dX]$/.test($.trim()))return"ORCID must be in format 0000-0000-0000-000X";return!0}},{type:"input",name:"description",message:"Why do you need access to NEMAR? (1-2 sentences):",validate:($)=>{let J=$?.trim();if(!J||J.length<20)return"Please provide at least 20 characters describing why you need NEMAR access";if(J.length>500)return"Description must be at most 500 characters";return!0}}]),F=N("Creating account...").start();try{let $=await E_({username:D.username,email:D.email,password:D.password,github_username:D.github_username,description:D.description.trim(),orcid:D.orcid?.trim()||void 0});F.succeed("Account created"),console.log(),console.log(H.green("Registration successful!")),console.log(),console.log("Next steps:"),$.next_steps.forEach((J,Q)=>{console.log(`  ${Q+1}. ${J}`)}),console.log(),console.log(H.dim("Once approved, use 'nemar auth retrieve-key' to get your API key"))}catch($){if($ instanceof i){if(F.fail($.message),$.details&&Array.isArray($.details))$.details.forEach((J)=>{console.log(H.dim(`  - ${J}`))});if($.message.includes("already taken"))console.log(H.dim("  Try a different username"));else if($.message.includes("already registered"))console.log(H.dim("  Use 'nemar auth resend-verification' if you need a new verification link"))}else F.fail("Registration failed"),console.log(H.dim(`  ${$ instanceof Error?$.message:"Unknown error"}`))}}D1.command("signup").description("Register for a new NEMAR account").action(iJ);async function aJ(D){if(!v0()){console.log(H.yellow("Not authenticated")),console.log(),console.log("  Run 'nemar auth login' to authenticate"),console.log("  Run 'nemar auth signup' to create an account");return}let F;if(D.refresh){let B=N("Fetching user info...").start();try{let Y=await xJ();l8("username",Y.username),l8("email",Y.email),l8("githubUsername",Y.github_username),F=Y.role,B.stop()}catch(Y){if(B.fail("Could not refresh user info"),Y instanceof i&&Y.statusCode===401)console.log(H.dim("  Your session may have expired. Try logging in again."))}}let $=YD();if(console.log(H.green("Authenticated")),console.log(),$.username)console.log(`  Username: ${H.cyan($.username)}`);if($.email)console.log(`  Email:    ${$.email}`);if($.githubUsername)console.log(`  GitHub:   @${$.githubUsername}`);if(F){let B=F==="owner"?H.red("Owner"):F==="admin"?H.magenta("Admin"):H.white("Member");console.log(`  Role:     ${B}`)}console.log(`  Config:   ${H.dim(B_())}`);let Q=V9().filter((B)=>!B.active);if(Q.length>0)console.log(),console.log(`  Other accounts: ${Q.map((B)=>H.dim(B.username)).join(", ")}`),console.log(H.dim("  Run 'nemar auth switch' to switch accounts"))}D1.command("status").description("Check current authentication status").option("--refresh","Refresh user info from server").action(aJ);D1.command("whoami").description("Show current user (alias for status)").option("--refresh","Refresh user info from server").action(aJ);async function aK0(D){try{let F=Bun.which("gh");if(!F){console.log(H.dim("  GitHub CLI (gh) not found in PATH, skipping"));return}let $=Bun.spawn({cmd:[F,"auth","switch","--user",D],stdout:"pipe",stderr:"pipe"}),J=await new Response($.stderr).text(),Q=await $.exited;if(Q===0)console.log(`  GitHub CLI switched to ${H.cyan(`@${D}`)}`);else{let B=J.trim();if(B.includes("not found")||B.includes("no accounts"))console.log(H.dim(`  GitHub CLI: @${D} not logged in (run 'gh auth login')`));else console.log(H.dim(`  GitHub CLI switch failed: ${B||`exit code ${Q}`}`))}}catch(F){let $=F instanceof Error?F.message:String(F);console.log(H.dim(`  GitHub CLI switch skipped: ${$}`))}}async function EW(D){let F=V9();if(F.length===0){console.log(H.yellow("No stored accounts")),console.log("  Run 'nemar auth login' to add an account");return}if(F.length===1){let B=F[0];if(B.active){console.log(H.yellow(`Only one account stored: ${B.username}`)),console.log("  Run 'nemar auth login' to add another account");return}}let $;if(D)$=D;else{let B=F.map((X)=>({name:`${X.username}${X.githubUsername?` (@${X.githubUsername})`:""}${X.active?H.green(" (active)"):""}`,value:X.username,short:X.username})),{selected:Y}=await B0.prompt([{type:"list",name:"selected",message:"Switch to account:",choices:B,default:F.find((X)=>X.active)?.username}]);$=Y}let J=F.find((B)=>B.active);if(J&&J.username===$){console.log(H.yellow(`Already using account ${$}`));return}let Q=X_($);if(!Q){console.log(H.red(`Account not found: ${$}`)),console.log(H.dim("  Provide a NEMAR username or GitHub username")),console.log(H.dim(`  Available: ${F.map((B)=>B.username).join(", ")}`));return}if(console.log(H.green(`Switched to ${H.cyan(Q.username||$)}`)),Q.githubUsername)await aK0(Q.githubUsername)}var oK0=D1.command("switch [username]").description("Switch between stored accounts").action(EW);m6(oK0,`
 Description:
   Switch the active NEMAR account. You can specify a NEMAR username or
   GitHub username. If no username is given, an interactive picker is shown.
@@ -398,22 +398,20 @@ Description:
 Examples:
   $ nemar auth switch              # Interactive picker
   $ nemar auth switch yahya        # Switch by NEMAR username
-  $ nemar auth switch cool-vibers  # Switch by GitHub username`);async function zW(D){if(!v0()){console.log(H.yellow("Not currently authenticated"));return}if(D.all){let Q=V9();if(await y0(`Log out all ${Q.length} stored account(s)?`,D)!=="confirmed")return;Q_(),console.log(H.green("All accounts removed"));return}let F=YD();if(await y0(`Log out ${F.username||"current user"}?`,D)!=="confirmed")return;J_(),console.log(H.green("Logged out successfully"));let J=V9();if(J.length>0){let Q=J.find((B)=>B.active);if(Q)console.log(`  Switched to ${H.cyan(Q.username)}`)}}D1.command("logout").description("Remove the active account (use --all to remove all)").option(I0,S0).option(a0,g0).option("--all","Remove all stored accounts").action(zW);D1.command("resend-verification").description("Resend email verification link").action(async()=>{let{email:D}=await B0.prompt([{type:"input",name:"email",message:"Enter your email address:",validate:($)=>{if(!$||!/^[^\s@]+@[^\s@]+\.[^\s@]+$/.test($))return"Please enter a valid email address";return!0}}]),F=N("Sending verification email...").start();try{let $=await V_(D);F.succeed($.message)}catch($){if($ instanceof i){if(F.fail($.message),$.statusCode===0)console.log(H.gray("  Check your internet connection"))}else F.fail(`Failed to send verification email: ${$ instanceof Error?$.message:"Unknown error"}`),console.log(H.gray("  Check your internet connection"))}});async function sK0(D){if(!v0()){console.log(H.yellow("Not authenticated")),console.log(),console.log("  Run 'nemar auth login' first to authenticate");return}let F=YD();if(!D.force){let G=N("Checking existing SSH access...").start(),W=await qW();if(W.success){if(G.succeed("SSH access to GitHub already configured"),W.username)console.log(`  GitHub user: ${H.cyan(W.username)}`);console.log(),console.log(H.gray("Use --force to regenerate SSH key anyway"));return}G.info("SSH access to GitHub not configured")}console.log(),console.log(H.cyan("Setting up SSH access for GitHub")),console.log(H.gray(`This will generate a dedicated SSH key for NEMAR uploads
-`));let $=null,J=I4();if(ff()&&!D.force)console.log(H.gray(`  Using existing key: ${J.privateKey}`)),$=hf();else{let G=N("Generating SSH key...").start(),W=await gf(F.email||"nemar-user");if(!W.success){G.fail("Failed to generate SSH key"),console.log(H.gray(`  ${W.error}`));return}G.succeed("SSH key generated"),console.log(H.gray(`  Private key: ${J.privateKey}`)),console.log(H.gray(`  Public key: ${J.publicKey}`)),$=W.publicKey||null}if(!$){console.log(H.red("Could not read public key"));return}let Q=N("Configuring SSH...").start(),B=bf();if(!B.success){Q.fail("Failed to configure SSH"),console.log(H.gray(`  ${B.error}`));return}Q.succeed("SSH configured for GitHub"),console.log();let Y=N("Testing SSH connection to GitHub...").start(),X=await qW();if(X.success){if(Y.succeed("SSH connection verified"),X.username)console.log(`  GitHub user: ${H.cyan(X.username)}`);console.log(),console.log(H.green("SSH setup complete! You can now upload datasets."));return}Y.info("SSH key generated but not yet added to GitHub"),console.log(),console.log(H.yellow("To complete setup, add this SSH key to your GitHub account:")),console.log(),console.log(H.cyan(`  ${$}`)),console.log(),console.log("Steps:"),console.log("  1. Copy the key above"),console.log(`  2. Go to: ${H.underline("https://github.com/settings/ssh/new")}`),console.log(`  3. Title: ${H.gray("NEMAR CLI")}`),console.log("  4. Paste the key and click 'Add SSH key'"),console.log(),console.log(H.gray("After adding the key, run 'nemar auth setup-ssh' again to verify."))}var rK0=D1.command("setup-ssh").description("Configure SSH access for GitHub (auto-generates key)").option("-f, --force","Regenerate SSH key even if one exists").action(sK0);m6(rK0,`
+  $ nemar auth switch cool-vibers  # Switch by GitHub username`);async function zW(D){if(!v0()){console.log(H.yellow("Not currently authenticated"));return}if(D.all){let Q=V9();if(await y0(`Log out all ${Q.length} stored account(s)?`,D)!=="confirmed")return;Q_(),console.log(H.green("All accounts removed"));return}let F=YD();if(await y0(`Log out ${F.username||"current user"}?`,D)!=="confirmed")return;J_(),console.log(H.green("Logged out successfully"));let J=V9();if(J.length>0){let Q=J.find((B)=>B.active);if(Q)console.log(`  Switched to ${H.cyan(Q.username)}`)}}D1.command("logout").description("Remove the active account (use --all to remove all)").option(I0,S0).option(a0,g0).option("--all","Remove all stored accounts").action(zW);D1.command("resend-verification").description("Resend email verification link").action(async()=>{let{email:D}=await B0.prompt([{type:"input",name:"email",message:"Enter your email address:",validate:($)=>{if(!$||!/^[^\s@]+@[^\s@]+\.[^\s@]+$/.test($))return"Please enter a valid email address";return!0}}]),F=N("Sending verification email...").start();try{let $=await V_(D);F.succeed($.message)}catch($){if($ instanceof i){if(F.fail($.message),$.statusCode===0)console.log(H.dim("  Check your internet connection"))}else F.fail(`Failed to send verification email: ${$ instanceof Error?$.message:"Unknown error"}`),console.log(H.dim("  Check your internet connection"))}});async function sK0(D){if(!v0()){console.log(H.yellow("Not authenticated")),console.log(),console.log("  Run 'nemar auth login' first to authenticate");return}let F=YD();if(!D.force){let G=N("Checking existing SSH access...").start(),W=await qW();if(W.success){if(G.succeed("SSH access to GitHub already configured"),W.username)console.log(`  GitHub user: ${H.cyan(W.username)}`);console.log(),console.log(H.dim("Use --force to regenerate SSH key anyway"));return}G.info("SSH access to GitHub not configured")}console.log(),console.log(H.cyan("Setting up SSH access for GitHub")),console.log(H.dim(`This will generate a dedicated SSH key for NEMAR uploads
+`));let $=null,J=I4();if(ff()&&!D.force)console.log(H.dim(`  Using existing key: ${J.privateKey}`)),$=hf();else{let G=N("Generating SSH key...").start(),W=await gf(F.email||"nemar-user");if(!W.success){G.fail("Failed to generate SSH key"),console.log(H.dim(`  ${W.error}`));return}G.succeed("SSH key generated"),console.log(H.dim(`  Private key: ${J.privateKey}`)),console.log(H.dim(`  Public key: ${J.publicKey}`)),$=W.publicKey||null}if(!$){console.log(H.red("Could not read public key"));return}let Q=N("Configuring SSH...").start(),B=bf();if(!B.success){Q.fail("Failed to configure SSH"),console.log(H.dim(`  ${B.error}`));return}Q.succeed("SSH configured for GitHub"),console.log();let Y=N("Testing SSH connection to GitHub...").start(),X=await qW();if(X.success){if(Y.succeed("SSH connection verified"),X.username)console.log(`  GitHub user: ${H.cyan(X.username)}`);console.log(),console.log(H.green("SSH setup complete! You can now upload datasets."));return}Y.info("SSH key generated but not yet added to GitHub"),console.log(),console.log(H.yellow("To complete setup, add this SSH key to your GitHub account:")),console.log(),console.log(H.cyan(`  ${$}`)),console.log(),console.log("Steps:"),console.log("  1. Copy the key above"),console.log(`  2. Go to: ${H.underline("https://github.com/settings/ssh/new")}`),console.log(`  3. Title: ${H.dim("NEMAR CLI")}`),console.log("  4. Paste the key and click 'Add SSH key'"),console.log(),console.log(H.dim("After adding the key, run 'nemar auth setup-ssh' again to verify."))}var rK0=D1.command("setup-ssh").description("Configure SSH access for GitHub (optional, gh CLI preferred)").option("-f, --force","Regenerate SSH key even if one exists").action(sK0);m6(rK0,`
 Description:
-  Automatically configures SSH access for GitHub, which is required
-  for uploading datasets. This command will:
+  Configures SSH access for GitHub as an alternative to gh CLI (HTTPS).
+  Most users should use 'gh auth login' instead; SSH is only needed if
+  you cannot use the GitHub CLI.
   1. Generate a dedicated Ed25519 SSH key for NEMAR (~/.ssh/nemar_ed25519)
   2. Configure SSH to use this key for GitHub
   3. Verify the connection (prompts you to add the key to GitHub if needed)
-  This is a one-time setup. After running this command and adding the key
-  to GitHub, you can upload datasets.
 Examples:
   $ nemar auth setup-ssh          # Set up SSH access
-  $ nemar auth setup-ssh --force  # Regenerate key even if exists`);var tK0=D1.command("retrieve-key").description("Retrieve your API key after account approval (requires email and password)").action(async()=>{let D=await B0.prompt([{type:"input",name:"email",message:"Email address:",validate:($)=>{if(!$||!/^[^\s@]+@[^\s@]+\.[^\s@]+$/.test($))return"Please enter a valid email address";return!0}},{type:"password",name:"password",message:"Password:",mask:"*",validate:($)=>{if(!$)return"Password is required";return!0}}]),F=N("Retrieving API key...").start();try{let $=await Z_(D.email,D.password);F.succeed("API key retrieved"),console.log(),console.log(H.yellow("Your API Key (store this securely):")),console.log(H.gray(`  ${$.api_key}`)),console.log(),console.log("Next step:"),console.log(`  Run ${H.cyan("nemar auth login")} and paste your API key`)}catch($){if($ instanceof i){if($.statusCode===409){let J=$.details;if(F.info("API key already issued"),J?.api_key_prefix)console.log(),console.log(`  Key prefix: ${H.gray(J.api_key_prefix)}`);console.log(),console.log("  If you lost your API key, regenerate it:"),console.log(`  ${H.cyan("nemar auth regenerate-key")}`)}else if(F.fail($.message),$.statusCode===401)console.log(H.gray("  Check your email and password"));else if($.statusCode===403)console.log(H.gray("  Your account may not be approved yet"))}else{let J=$ instanceof Error?$.message:"Unknown error";F.fail(`Failed to retrieve API key: ${J}`)}}});m6(tK0,`
+  $ nemar auth setup-ssh --force  # Regenerate key even if exists`);var tK0=D1.command("retrieve-key").description("Retrieve your API key after account approval (requires email and password)").action(async()=>{let D=await B0.prompt([{type:"input",name:"email",message:"Email address:",validate:($)=>{if(!$||!/^[^\s@]+@[^\s@]+\.[^\s@]+$/.test($))return"Please enter a valid email address";return!0}},{type:"password",name:"password",message:"Password:",mask:"*",validate:($)=>{if(!$)return"Password is required";return!0}}]),F=N("Retrieving API key...").start();try{let $=await Z_(D.email,D.password);F.succeed("API key retrieved"),console.log(),console.log(H.yellow("Your API Key (store this securely):")),console.log(H.dim(`  ${$.api_key}`)),console.log(),console.log("Next step:"),console.log(`  Run ${H.cyan("nemar auth login")} and paste your API key`)}catch($){if($ instanceof i){if($.statusCode===409){let J=$.details;if(F.info("API key already issued"),J?.api_key_prefix)console.log(),console.log(`  Key prefix: ${H.dim(J.api_key_prefix)}`);console.log(),console.log("  If you lost your API key, regenerate it:"),console.log(`  ${H.cyan("nemar auth regenerate-key")}`)}else if(F.fail($.message),$.statusCode===401)console.log(H.dim("  Check your email and password"));else if($.statusCode===403)console.log(H.dim("  Your account may not be approved yet"))}else{let J=$ instanceof Error?$.message:"Unknown error";F.fail(`Failed to retrieve API key: ${J}`)}}});m6(tK0,`
 Description:
   After an admin approves your account, use this command to securely
   retrieve your API key. You will need the email and password you used
@@ -423,8 +421,8 @@ Description:
   to obtain your key.
 Examples:
-  $ nemar auth retrieve-key`);var eK0=D1.command("regenerate-key").description("Request a new API key (revokes current key, requires email verification)").action(async()=>{console.log(H.yellow("API Key Regeneration")),console.log(H.gray(`This will revoke your current key and generate a new one
-`));let{email:D}=await B0.prompt([{type:"input",name:"email",message:"Email address associated with your account:",validate:($)=>{if(!$||!/^[^\s@]+@[^\s@]+\.[^\s@]+$/.test($))return"Please enter a valid email address";return!0}}]),F=N("Sending verification email...").start();try{let $=await U_(D);F.succeed("Verification email sent"),console.log(),console.log("Next steps:"),console.log("  1. Check your email for a verification link"),console.log("  2. Click the link to generate your new API key"),console.log("  3. Copy the new key and run 'nemar auth login'"),console.log(),console.log(H.gray("The link expires in 1 hour"))}catch($){if($ instanceof i)F.fail($.message);else F.fail("Failed to send verification email"),console.log(H.gray("  Check your internet connection"))}});m6(eK0,`
+  $ nemar auth retrieve-key`);var eK0=D1.command("regenerate-key").description("Request a new API key (revokes current key, requires email verification)").action(async()=>{console.log(H.yellow("API Key Regeneration")),console.log(H.dim(`This will revoke your current key and generate a new one
+`));let{email:D}=await B0.prompt([{type:"input",name:"email",message:"Email address associated with your account:",validate:($)=>{if(!$||!/^[^\s@]+@[^\s@]+\.[^\s@]+$/.test($))return"Please enter a valid email address";return!0}}]),F=N("Sending verification email...").start();try{let $=await U_(D);F.succeed("Verification email sent"),console.log(),console.log("Next steps:"),console.log("  1. Check your email for a verification link"),console.log("  2. Click the link to generate your new API key"),console.log("  3. Copy the new key and run 'nemar auth login'"),console.log(),console.log(H.dim("The link expires in 1 hour"))}catch($){if($ instanceof i)F.fail($.message);else F.fail("Failed to send verification email"),console.log(H.dim("  Check your internet connection"))}});m6(eK0,`
 Description:
   If you lost your API key or it was compromised, use this command to
   request a new one. A verification email will be sent to confirm the
@@ -504,7 +502,7 @@ Description:
 Requirements:
   - NEMAR account (nemar auth login)
   - git-annex installed
-  - GitHub SSH access configured
+  - GitHub CLI authenticated (gh auth login)
 Process:
   1. Validates BIDS format (unless --skip-validation)
@@ -521,14 +519,14 @@ Examples:
   $ nemar dataset upload ./my-eeg-dataset
   $ nemar dataset upload ./ds -n "My EEG Study" -d "64-channel EEG data"
   $ nemar dataset upload ./ds --dry-run        # Preview without uploading
-  $ nemar dataset upload ./ds -j 16            # More parallel streams`).action(async(D,F)=>{let $=YD();if(!v0())console.log(H.red("Error: Not authenticated")),console.log("Run 'nemar auth login' first"),process.exit(1);if(!$_())console.log(H.yellow("Sandbox training required")),console.log(),console.log("You must complete sandbox training before uploading real datasets."),console.log("This verifies your setup and familiarizes you with the workflow."),console.log(),console.log("Run sandbox training with:"),console.log(H.cyan("  nemar sandbox")),process.exit(1);let J=$D(D);if(!JD(J))console.log(H.red(`Error: Path does not exist: ${J}`)),process.exit(1);await rJ("upload");let Q=N("Checking prerequisites...").start(),B=await uJ();if(!B.allPassed){Q.fail("Prerequisites check failed"),console.log();for(let R of B.errors)console.log(H.red(`  - ${R}`));process.exit(1)}if(Q.succeed("Prerequisites check passed"),console.log(H.gray(`  git-annex ${B.gitAnnex.version}`)),B.githubSSH.username)console.log(H.gray(`  GitHub SSH: ${B.githubSSH.username}`));console.log(),Q=N("Verifying GitHub CLI authentication...").start();let Y=await mJ($.githubUsername);if(!Y.authenticated)Q.fail("GitHub CLI not authenticated"),console.log(H.red(`  ${Y.error}`)),console.log(),console.log("GitHub CLI is required for dataset uploads. Install and authenticate:"),console.log(H.cyan("  brew install gh       # or visit https://cli.github.com/")),console.log(H.cyan("  gh auth login")),process.exit(1);if($.githubUsername&&!Y.matches)Q.warn("GitHub CLI user mismatch"),console.log(H.yellow(`  ${Y.error}`)),console.log(),console.log("Your gh CLI is authenticated as a different GitHub account than your NEMAR account."),console.log("This may cause issues with repository access. To fix:"),console.log(H.cyan(`  gh auth login    # Login as ${$.githubUsername}`)),console.log(),console.log(H.yellow("WARNING: If upload fails with permission errors, this mismatch is the likely cause.")),console.log();else Q.succeed(`GitHub CLI authenticated as ${Y.username}`);if(!F.skipValidation){Q=N("Validating BIDS dataset...").start();let R=$D(J,"dataset_description.json");if(!JD(R))Q.fail("Not a valid BIDS dataset"),console.log(H.red("Missing required file: dataset_description.json")),process.exit(1);if(!(await j9()).installed)Q.fail("Deno is required for BIDS validation"),console.log(),console.log(H.red("Error: Deno is not installed")),console.log(),console.log("The BIDS validator requires Deno runtime to run."),console.log("Install Deno with one of these commands:"),console.log(),console.log(H.cyan("  # macOS/Linux (curl)")),console.log("  curl -fsSL https://deno.land/install.sh | sh"),console.log(),console.log(H.cyan("  # macOS (Homebrew)")),console.log("  brew install deno"),console.log(),console.log(H.cyan("  # Windows (PowerShell)")),console.log("  irm https://deno.land/install.ps1 | iex"),console.log(),console.log("Learn more: https://docs.deno.com/runtime/getting_started/installation/"),console.log(),console.log(H.gray("To skip validation (not recommended): nemar dataset upload --skip-validation")),process.exit(1);try{let d=await mf(J,{prune:!0});if(!d.valid)Q.fail("Dataset has validation errors"),console.log(),console.log(pf(d)),console.log(),console.log(H.yellow("Fix the errors above before uploading.")),console.log(H.gray("Or use --skip-validation to upload anyway (not recommended).")),process.exit(1);Q.succeed(`Dataset is valid BIDS (${d.warningCount} warnings)`)}catch(d){Q.fail("Validation failed"),console.log(H.red(d.message)),process.exit(1)}console.log()}Q=N("Analyzing dataset files...").start();let X={};try{let R=$D(J,"dataset_description.json");X=JSON.parse(L8(R,"utf-8"))}catch(R){if(R.code!=="ENOENT")console.log(H.yellow(`Warning: Could not read dataset_description.json: ${R.message}`))}let G=F.name||(typeof X.Name==="string"?X.Name:null)||vE0(J),W=await Vf(J);Q.succeed(`Found ${W.files.length} files (${W.dataFiles} data, ${W.metadataFiles} metadata)`);let q,K=$D(J,".nemar","metadata.json"),Z=$D(J,"nemar_metadata.json");if(JD(K))try{q=JSON.parse(L8(K,"utf-8")),console.log(H.gray("  Using existing .nemar/metadata.json (author ORCIDs from prior run)"))}catch(R){console.log(H.yellow(`  Warning: Could not read .nemar/metadata.json: ${R instanceof Error?R.message:R}. 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Will re-collect author information.`))}if(!q&&!F.skipOrcid&&process.stdin.isTTY){let R=X.Authors,A0=Array.isArray(R)?R.filter((d)=>typeof d==="string"):[];if(A0.length>0)try{let d,p;try{let K0=await xJ();d=K0.orcid||void 0,p=K0.username}catch(K0){console.log(H.gray(`  Could not fetch profile: ${p0(K0)}`))}console.log(),console.log(H.cyan("Authors found:"),A0.join(" | "));let W0={},w0;if(d&&p){let K0=p.toLowerCase(),XD=A0.find((x0)=>x0.toLowerCase().includes(K0));if(XD)W0[XD]={orcid:d},w0=XD,console.log(`  Your ORCID (from profile): ${H.green(d)} (matched to "${XD}")`)}try{let{discoverOrcidsFromReferencedDois:K0}=await Promise.resolve().then(() => (Cg(),Ng)),XD=N("Looking up author ORCIDs from referenced publications...").start(),x0=await K0(X,W0),$1=Object.keys(x0.discoveries).length;if($1>0){XD.succeed(`Found ${$1} ORCID(s) from referenced DOIs`);for(let[M8,N8]of Object.entries(x0.discoveries))console.log(`  ${H.green(N8.orcid)} -> "${M8}" (from ${N8.sourceDoi}, ${N8.confidence} match)`);let{confirmOrcids:GD}=await B0.prompt([{type:"confirm",name:"confirmOrcids",message:"Accept these auto-discovered ORCIDs?",default:!0}]);if(GD)for(let[M8,N8]of Object.entries(x0.discoveries))W0[M8]={...W0[M8],orcid:N8.orcid,...N8.affiliations&&{affiliations:N8.affiliations}}}else XD.info("No ORCIDs found from referenced DOIs")}catch(K0){console.log(H.yellow(`  Could not auto-discover ORCIDs: ${p0(K0)}`))}for(let K0 of A0){if(K0===w0)continue;if(W0[K0]?.orcid)continue;let{orcid:XD}=await B0.prompt([{type:"input",name:"orcid",message:`ORCID for "${K0}" (Enter to skip):`,validate:(x0)=>{if(!x0)return!0;return yJ.test(x0)||"Invalid ORCID format (XXXX-XXXX-XXXX-XXXX)"}}]);if(XD){let x0={orcid:XD},{affiliation:$1}=await B0.prompt([{type:"input",name:"affiliation",message:`  Affiliation for "${K0}" (optional):`}]);if($1)x0.affiliations=[{name:$1}];W0[K0]=x0}}if(Object.keys(W0).length>0){q={version:"2.0",authors:W0};try{let K0=$D(J,".nemar");if(!JD(K0))Rg(K0,{recursive:!0});let XD=$D(K0,"metadata.json");k4(XD,JSON.stringify(q,null,2)),console.log(H.gray("  Saved .nemar/metadata.json with author ORCIDs"))}catch(K0){console.log(H.yellow(`  Warning: Could not save .nemar/metadata.json: ${p0(K0)}`))}}console.log()}catch(d){if(d instanceof i)console.log(H.yellow(`  Could not fetch profile: ${d.message}`));else console.log(H.yellow(`  Could not collect ORCIDs: ${p0(d)}`));console.log(H.gray("  Continuing without author enrichment."))}}let z;if(process.stdin.isTTY&&!F.skipValidation){let R=rf(J);if(R.spdxId){if(console.log(),console.log(H.cyan("License detected:"),H.bold(R.spdxId),H.gray(`(from ${R.source==="dataset_description"?"dataset_description.json":"LICENSE file"})`)),!tf(R.spdxId))console.log(H.yellow(`  Warning: "${R.spdxId}" is not in the list of known research-compatible licenses.`));let{keepLicense:d}=await B0.prompt([{type:"confirm",name:"keepLicense",message:`Use "${R.spdxId}" as the dataset license?`,default:!0}]);if(d)z=R.spdxId;else z=await OW(R.spdxId)}else{if(console.log(),R.source==="license_file")console.log(H.yellow("A LICENSE file was found but the license could not be identified automatically."));else console.log(H.yellow("No license found in this dataset."));console.log(H.gray("A license is required to publish on NEMAR.")),z=await OW()}try{let d=$D(J,"dataset_description.json");if(JD(d)){if(JSON.parse(L8(d,"utf-8")).License!==z)Dg(J,z),console.log(H.gray(`  Updated dataset_description.json License -> ${z}`))}}catch(d){console.log(H.yellow(`  Warning: Could not update license in dataset_description.json: ${p0(d)}`))}if(ef(J,z))console.log(H.gray(`  Created LICENSE file (${z})`));console.log()}if(process.stdin.isTTY&&!F.skipValidation&&z){let R=await Fg(z);if(R.isDerived&&R.sourceDatasets&&R.sourceDatasets.length>0){try{let A0=$D(J,"dataset_description.json");if(JD(A0)){let d=JSON.parse(L8(A0,"utf-8")),p=Array.isArray(d.SourceDatasets)?d.SourceDatasets:[],W0=R.sourceDatasets.map((K0)=>K0.identifier),w0=Array.from(new Set([...p,...W0]));d.SourceDatasets=w0,k4(A0,`${JSON.stringify(d,null,2)}
-`),console.log(H.gray(`  Updated dataset_description.json SourceDatasets (${w0.length} source(s))`))}}catch(A0){console.log(H.yellow(`  Warning: Could not update SourceDatasets: ${p0(A0)}`))}console.log()}}let U=MW(J);if(console.log(),U)console.log(H.bold.yellow("Resume Upload:")),console.log(`  Dataset ID: ${H.cyan(U.dataset_id)}`),console.log(`  Last attempt: ${U.last_upload_at||U.created_at}`);else console.log(H.bold("Upload Plan:"));if(console.log(`  Name: ${G}`),console.log(`  Path: ${J}`),console.log(`  Files: ${W.files.length}`),console.log(`  Size: ${V8(W.totalSize)}`),console.log(`  Data files: ${W.dataFiles} (will be uploaded to S3)`),console.log(`  Metadata files: ${W.metadataFiles} (will be stored in git)`),console.log(`  Parallel jobs: ${F.jobs}`),console.log(),F.dryRun){console.log(H.yellow("Dry run mode - no changes made"));return}let A=await y0("Proceed with upload?",{yes:F.yes,no:F.no},!0);if(A!=="confirmed"){console.log(A==="declined"?"Upload skipped.":"Upload cancelled.");return}console.log();let M=W.files.filter((R)=>R.type==="data");if(F.restart)eJ(J),console.log(H.gray("  Upload progress cleared (--restart)")),console.log();let L=F.restart?null:Bg(J);if(L){let R=Gg(L);if(console.log(H.bold.cyan("Upload Progress:")),console.log(`  Files: ${R.uploaded}/${R.total} uploaded, ${R.failed} failed, ${R.pending} pending`),R.completedSteps.length>0)console.log(`  Completed steps: ${R.completedSteps.join(", ")}`);console.log()}let C=L?Xg(L,M):M,O;if(U!==null){Q=N(`Resuming upload for ${U.dataset_id}...`).start();try{await cD(U.dataset_id),O={dataset_id:U.dataset_id,ssh_url:U.ssh_url,s3_prefix:U.s3_prefix,github_url:U.github_url,upload_urls:{},s3_config:U.s3_config},Q.succeed(`Resuming upload: ${O.dataset_id}`)}catch(R){if(Q.fail("Failed to resume upload"),R instanceof i){if(console.log(H.red(`  ${R.message}`)),R.statusCode===404)console.log(H.yellow("  The dataset may have been deleted. Try uploading as a new dataset.")),console.log(H.gray(`  Remove ${J}/.nemar to start fresh.`))}else console.log(H.red(`  ${R.message}`));process.exit(1)}}else{Q=N("Creating dataset in NEMAR...").start();try{let R=await _J({name:G,description:F.description,files:M.map((d)=>({path:d.path,size:d.size,type:d.type}))});O={dataset_id:R.dataset.dataset_id,ssh_url:R.dataset.ssh_url,s3_prefix:R.dataset.s3_prefix,github_url:R.dataset.github_url,upload_urls:R.upload_urls||{},s3_config:R.s3_config};let A0={dataset_id:O.dataset_id,github_url:O.github_url,ssh_url:O.ssh_url,s3_prefix:O.s3_prefix,s3_config:O.s3_config,created_at:new Date().toISOString()};NW(J,A0),Q.succeed(`Dataset created: ${O.dataset_id}`),await new Promise((d)=>setTimeout(d,1e4))}catch(R){if(Q.fail("Failed to create dataset"),R instanceof i)console.log(H.red(`  ${R.message}`));else console.log(H.red(`  ${R.message}`));process.exit(1)}}if(L&&L.dataset_id!==O.dataset_id)console.log(H.yellow("  Progress file is for a different dataset; starting fresh.")),eJ(J),L=null;Q=N("Accepting GitHub repository invitation...").start();let w=O.github_url?.match(/github\.com\/([a-zA-Z0-9_.-]+\/[a-zA-Z0-9_.-]+)/),I=w?w[1].replace(/\.git$/,""):null;if(!I)Q.fail("Invalid GitHub repository URL from backend"),console.log(H.red(`  Received: ${O.github_url||"(empty)"}`)),console.log(H.red("  Expected format: https://github.com/owner/repo")),console.log(),console.log("This may indicate a backend issue. Please contact support."),process.exit(1);let T=await lJ(I);if(T.accepted)if(T.alreadyCollaborator)Q.succeed("Already a collaborator on this repository");else Q.succeed("GitHub invitation accepted");else Q.warn("Could not auto-accept invitation"),console.log(H.yellow(`  ${T.error}`)),console.log(),console.log("You may need to accept the invitation manually:"),console.log(H.cyan(`  https://github.com/${I}/invitations`)),console.log();Q=N("Initializing git-annex dataset...").start();let f=$.username&&$.email?{name:$.username,email:$.email}:void 0;if(!await p8(J)){let R=await zF(J,{author:f});if(!R.success)Q.fail("Failed to initialize git-annex dataset"),console.log(H.red(`  ${R.error}`)),process.exit(1)}let s=await Qf(J);if(!s.success)Q.fail("Failed to initialize git-annex"),console.log(H.red(`  ${s.error}`)),process.exit(1);let h=await VF(J);if(!h.success)Q.warn("Could not configure largefiles pattern"),console.log(H.gray(`  ${h.error}`));Q.succeed("git-annex dataset initialized");try{let R=$D(J,".gitignore"),A0="";if(JD(R))A0=L8(R,"utf-8");if(!A0.includes(".nemar/")){let d=A0?`${A0.trimEnd()}
+  $ nemar dataset upload ./ds -j 16            # More parallel streams`).action(async(D,F)=>{let $=YD();if(!v0())console.log(H.red("Error: Not authenticated")),console.log("Run 'nemar auth login' first"),process.exit(1);if(!$_())console.log(H.yellow("Sandbox training required")),console.log(),console.log("You must complete sandbox training before uploading real datasets."),console.log("This verifies your setup and familiarizes you with the workflow."),console.log(),console.log("Run sandbox training with:"),console.log(H.cyan("  nemar sandbox")),process.exit(1);let J=$D(D);if(!JD(J))console.log(H.red(`Error: Path does not exist: ${J}`)),process.exit(1);await rJ("upload");let Q=N("Checking prerequisites...").start(),B=await uJ();if(!B.allPassed){Q.fail("Prerequisites check failed"),console.log();for(let R of B.errors)console.log(H.red(`  - ${R}`));process.exit(1)}if(Q.succeed("Prerequisites check passed"),console.log(H.dim(`  git-annex ${B.gitAnnex.version}`)),B.githubSSH.username)console.log(H.dim(`  GitHub: ${B.githubSSH.username}`));console.log(),Q=N("Verifying GitHub CLI authentication...").start();let Y=await mJ($.githubUsername);if(!Y.authenticated)Q.fail("GitHub CLI not authenticated"),console.log(H.red(`  ${Y.error}`)),console.log(),console.log("GitHub CLI is required for dataset uploads. 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To fix:"),console.log(H.cyan(`  gh auth login    # Login as ${$.githubUsername}`)),console.log(),console.log(H.yellow("WARNING: If upload fails with permission errors, this mismatch is the likely cause.")),console.log();else Q.succeed(`GitHub CLI authenticated as ${Y.username}`);if(!F.skipValidation){Q=N("Validating BIDS dataset...").start();let R=$D(J,"dataset_description.json");if(!JD(R))Q.fail("Not a valid BIDS dataset"),console.log(H.red("Missing required file: dataset_description.json")),process.exit(1);if(!(await j9()).installed)Q.fail("Deno is required for BIDS validation"),console.log(),console.log(H.red("Error: Deno is not installed")),console.log(),console.log("The BIDS validator requires Deno runtime to run."),console.log("Install Deno with one of these commands:"),console.log(),console.log(H.cyan("  # macOS/Linux (curl)")),console.log("  curl -fsSL https://deno.land/install.sh | sh"),console.log(),console.log(H.cyan("  # macOS (Homebrew)")),console.log("  brew install deno"),console.log(),console.log(H.cyan("  # Windows (PowerShell)")),console.log("  irm https://deno.land/install.ps1 | iex"),console.log(),console.log("Learn more: https://docs.deno.com/runtime/getting_started/installation/"),console.log(),console.log(H.dim("To skip validation (not recommended): nemar dataset upload --skip-validation")),process.exit(1);try{let d=await mf(J,{prune:!0});if(!d.valid)Q.fail("Dataset has validation errors"),console.log(),console.log(pf(d)),console.log(),console.log(H.yellow("Fix the errors above before uploading.")),console.log(H.dim("Or use --skip-validation to upload anyway (not recommended).")),process.exit(1);Q.succeed(`Dataset is valid BIDS (${d.warningCount} warnings)`)}catch(d){Q.fail("Validation failed"),console.log(H.red(d.message)),process.exit(1)}console.log()}Q=N("Analyzing dataset files...").start();let X={};try{let R=$D(J,"dataset_description.json");X=JSON.parse(L8(R,"utf-8"))}catch(R){if(R.code!=="ENOENT")console.log(H.yellow(`Warning: Could not read dataset_description.json: ${R.message}`))}let G=F.name||(typeof X.Name==="string"?X.Name:null)||vE0(J),W=await Vf(J);Q.succeed(`Found ${W.files.length} files (${W.dataFiles} data, ${W.metadataFiles} metadata)`);let q,K=$D(J,".nemar","metadata.json"),Z=$D(J,"nemar_metadata.json");if(JD(K))try{q=JSON.parse(L8(K,"utf-8")),console.log(H.dim("  Using existing .nemar/metadata.json (author ORCIDs from prior run)"))}catch(R){console.log(H.yellow(`  Warning: Could not read .nemar/metadata.json: ${R instanceof Error?R.message:R}. Will re-collect author information.`))}else if(JD(Z))try{q=JSON.parse(L8(Z,"utf-8")),console.log(H.dim("  Using existing nemar_metadata.json (author ORCIDs from prior run)"))}catch(R){console.log(H.yellow(`  Warning: Could not read nemar_metadata.json: ${R instanceof Error?R.message:R}. Will re-collect author information.`))}if(!q&&!F.skipOrcid&&process.stdin.isTTY){let R=X.Authors,A0=Array.isArray(R)?R.filter((d)=>typeof d==="string"):[];if(A0.length>0)try{let d,p;try{let K0=await xJ();d=K0.orcid||void 0,p=K0.username}catch(K0){console.log(H.dim(`  Could not fetch profile: ${p0(K0)}`))}console.log(),console.log(H.cyan("Authors found:"),A0.join(" | "));let W0={},w0;if(d&&p){let K0=p.toLowerCase(),XD=A0.find((x0)=>x0.toLowerCase().includes(K0));if(XD)W0[XD]={orcid:d},w0=XD,console.log(`  Your ORCID (from profile): ${H.green(d)} (matched to "${XD}")`)}try{let{discoverOrcidsFromReferencedDois:K0}=await Promise.resolve().then(() => (Cg(),Ng)),XD=N("Looking up author ORCIDs from referenced publications...").start(),x0=await K0(X,W0),$1=Object.keys(x0.discoveries).length;if($1>0){XD.succeed(`Found ${$1} ORCID(s) from referenced DOIs`);for(let[M8,N8]of Object.entries(x0.discoveries))console.log(`  ${H.green(N8.orcid)} -> "${M8}" (from ${N8.sourceDoi}, ${N8.confidence} match)`);let{confirmOrcids:GD}=await B0.prompt([{type:"confirm",name:"confirmOrcids",message:"Accept these auto-discovered ORCIDs?",default:!0}]);if(GD)for(let[M8,N8]of Object.entries(x0.discoveries))W0[M8]={...W0[M8],orcid:N8.orcid,...N8.affiliations&&{affiliations:N8.affiliations}}}else XD.info("No ORCIDs found from referenced DOIs")}catch(K0){console.log(H.yellow(`  Could not auto-discover ORCIDs: ${p0(K0)}`))}for(let K0 of A0){if(K0===w0)continue;if(W0[K0]?.orcid)continue;let{orcid:XD}=await B0.prompt([{type:"input",name:"orcid",message:`ORCID for "${K0}" (Enter to skip):`,validate:(x0)=>{if(!x0)return!0;return yJ.test(x0)||"Invalid ORCID format (XXXX-XXXX-XXXX-XXXX)"}}]);if(XD){let x0={orcid:XD},{affiliation:$1}=await B0.prompt([{type:"input",name:"affiliation",message:`  Affiliation for "${K0}" (optional):`}]);if($1)x0.affiliations=[{name:$1}];W0[K0]=x0}}if(Object.keys(W0).length>0){q={version:"2.0",authors:W0};try{let K0=$D(J,".nemar");if(!JD(K0))Rg(K0,{recursive:!0});let XD=$D(K0,"metadata.json");k4(XD,JSON.stringify(q,null,2)),console.log(H.dim("  Saved .nemar/metadata.json with author ORCIDs"))}catch(K0){console.log(H.yellow(`  Warning: Could not save .nemar/metadata.json: ${p0(K0)}`))}}console.log()}catch(d){if(d instanceof i)console.log(H.yellow(`  Could not fetch profile: ${d.message}`));else console.log(H.yellow(`  Could not collect ORCIDs: ${p0(d)}`));console.log(H.dim("  Continuing without author enrichment."))}}let z;if(process.stdin.isTTY&&!F.skipValidation){let R=rf(J);if(R.spdxId){if(console.log(),console.log(H.cyan("License detected:"),H.bold(R.spdxId),H.dim(`(from ${R.source==="dataset_description"?"dataset_description.json":"LICENSE file"})`)),!tf(R.spdxId))console.log(H.yellow(`  Warning: "${R.spdxId}" is not in the list of known research-compatible licenses.`));let{keepLicense:d}=await B0.prompt([{type:"confirm",name:"keepLicense",message:`Use "${R.spdxId}" as the dataset license?`,default:!0}]);if(d)z=R.spdxId;else z=await OW(R.spdxId)}else{if(console.log(),R.source==="license_file")console.log(H.yellow("A LICENSE file was found but the license could not be identified automatically."));else console.log(H.yellow("No license found in this dataset."));console.log(H.dim("A license is required to publish on NEMAR.")),z=await OW()}try{let d=$D(J,"dataset_description.json");if(JD(d)){if(JSON.parse(L8(d,"utf-8")).License!==z)Dg(J,z),console.log(H.dim(`  Updated dataset_description.json License -> ${z}`))}}catch(d){console.log(H.yellow(`  Warning: Could not update license in dataset_description.json: ${p0(d)}`))}if(ef(J,z))console.log(H.dim(`  Created LICENSE file (${z})`));console.log()}if(process.stdin.isTTY&&!F.skipValidation&&z){let R=await Fg(z);if(R.isDerived&&R.sourceDatasets&&R.sourceDatasets.length>0){try{let A0=$D(J,"dataset_description.json");if(JD(A0)){let d=JSON.parse(L8(A0,"utf-8")),p=Array.isArray(d.SourceDatasets)?d.SourceDatasets:[],W0=R.sourceDatasets.map((K0)=>K0.identifier),w0=Array.from(new Set([...p,...W0]));d.SourceDatasets=w0,k4(A0,`${JSON.stringify(d,null,2)}
+`),console.log(H.dim(`  Updated dataset_description.json SourceDatasets (${w0.length} source(s))`))}}catch(A0){console.log(H.yellow(`  Warning: Could not update SourceDatasets: ${p0(A0)}`))}console.log()}}let U=MW(J);if(console.log(),U)console.log(H.bold.yellow("Resume Upload:")),console.log(`  Dataset ID: ${H.cyan(U.dataset_id)}`),console.log(`  Last attempt: ${U.last_upload_at||U.created_at}`);else console.log(H.bold("Upload Plan:"));if(console.log(`  Name: ${G}`),console.log(`  Path: ${J}`),console.log(`  Files: ${W.files.length}`),console.log(`  Size: ${V8(W.totalSize)}`),console.log(`  Data files: ${W.dataFiles} (will be uploaded to S3)`),console.log(`  Metadata files: ${W.metadataFiles} (will be stored in git)`),console.log(`  Parallel jobs: ${F.jobs}`),console.log(),F.dryRun){console.log(H.yellow("Dry run mode - no changes made"));return}let A=await y0("Proceed with upload?",{yes:F.yes,no:F.no},!0);if(A!=="confirmed"){console.log(A==="declined"?"Upload skipped.":"Upload cancelled.");return}console.log();let M=W.files.filter((R)=>R.type==="data");if(F.restart)eJ(J),console.log(H.dim("  Upload progress cleared (--restart)")),console.log();let L=F.restart?null:Bg(J);if(L){let R=Gg(L);if(console.log(H.bold.cyan("Upload Progress:")),console.log(`  Files: ${R.uploaded}/${R.total} uploaded, ${R.failed} failed, ${R.pending} pending`),R.completedSteps.length>0)console.log(`  Completed steps: ${R.completedSteps.join(", ")}`);console.log()}let C=L?Xg(L,M):M,O;if(U!==null){Q=N(`Resuming upload for ${U.dataset_id}...`).start();try{await cD(U.dataset_id),O={dataset_id:U.dataset_id,ssh_url:U.ssh_url,s3_prefix:U.s3_prefix,github_url:U.github_url,upload_urls:{},s3_config:U.s3_config},Q.succeed(`Resuming upload: ${O.dataset_id}`)}catch(R){if(Q.fail("Failed to resume upload"),R instanceof i){if(console.log(H.red(`  ${R.message}`)),R.statusCode===404)console.log(H.yellow("  The dataset may have been deleted. Try uploading as a new dataset.")),console.log(H.dim(`  Remove ${J}/.nemar to start fresh.`))}else console.log(H.red(`  ${R.message}`));process.exit(1)}}else{Q=N("Creating dataset in NEMAR...").start();try{let R=await _J({name:G,description:F.description,files:M.map((d)=>({path:d.path,size:d.size,type:d.type}))});O={dataset_id:R.dataset.dataset_id,ssh_url:R.dataset.ssh_url,s3_prefix:R.dataset.s3_prefix,github_url:R.dataset.github_url,upload_urls:R.upload_urls||{},s3_config:R.s3_config};let A0={dataset_id:O.dataset_id,github_url:O.github_url,ssh_url:O.ssh_url,s3_prefix:O.s3_prefix,s3_config:O.s3_config,created_at:new Date().toISOString()};NW(J,A0),Q.succeed(`Dataset created: ${O.dataset_id}`),await new Promise((d)=>setTimeout(d,1e4))}catch(R){if(Q.fail("Failed to create dataset"),R instanceof i)console.log(H.red(`  ${R.message}`));else console.log(H.red(`  ${R.message}`));process.exit(1)}}if(L&&L.dataset_id!==O.dataset_id)console.log(H.yellow("  Progress file is for a different dataset; starting fresh.")),eJ(J),L=null;Q=N("Accepting GitHub repository invitation...").start();let w=O.github_url?.match(/github\.com\/([a-zA-Z0-9_.-]+\/[a-zA-Z0-9_.-]+)/),I=w?w[1].replace(/\.git$/,""):null;if(!I)Q.fail("Invalid GitHub repository URL from backend"),console.log(H.red(`  Received: ${O.github_url||"(empty)"}`)),console.log(H.red("  Expected format: https://github.com/owner/repo")),console.log(),console.log("This may indicate a backend issue. Please contact support."),process.exit(1);let T=await lJ(I);if(T.accepted)if(T.alreadyCollaborator)Q.succeed("Already a collaborator on this repository");else Q.succeed("GitHub invitation accepted");else Q.warn("Could not auto-accept invitation"),console.log(H.yellow(`  ${T.error}`)),console.log(),console.log("You may need to accept the invitation manually:"),console.log(H.cyan(`  https://github.com/${I}/invitations`)),console.log();Q=N("Initializing git-annex dataset...").start();let f=$.username&&$.email?{name:$.username,email:$.email}:void 0;if(!await p8(J)){let R=await zF(J,{author:f});if(!R.success)Q.fail("Failed to initialize git-annex dataset"),console.log(H.red(`  ${R.error}`)),process.exit(1)}let s=await Qf(J);if(!s.success)Q.fail("Failed to initialize git-annex"),console.log(H.red(`  ${s.error}`)),process.exit(1);let h=await VF(J);if(!h.success)Q.warn("Could not configure largefiles pattern"),console.log(H.dim(`  ${h.error}`));Q.succeed("git-annex dataset initialized");try{let R=$D(J,".gitignore"),A0="";if(JD(R))A0=L8(R,"utf-8");if(!A0.includes(".nemar/")){let d=A0?`${A0.trimEnd()}
 .nemar/
 `:`.nemar/
-`;k4(R,d)}}catch(R){console.log(H.yellow(`  Warning: Could not update .gitignore: ${p0(R)}`))}Q=N("Configuring GitHub remote...").start();let t=await f6(J,O.ssh_url);if(!t.success)Q.fail("Failed to configure GitHub remote"),console.log(H.red(`  ${t.error}`)),process.exit(1);if(Q.succeed("GitHub remote configured"),!await zf(J,{yes:F.yes}))process.exit(1);if(!L)L=Qg(J,O.dataset_id,M);else{for(let R of M)if(!L.files[R.path])L.files[R.path]={status:"pending",size:R.size,updated_at:new Date().toISOString()};p1(J,L)}if(!LF(L,"s3_upload")){if(C.length>0){Q=N("Requesting upload credentials...").start();let R;try{R=await R4(O.dataset_id),Q.succeed("Upload credentials received (2h expiry)")}catch(W0){Q.fail(`Could not get upload credentials: ${p0(W0)}`),console.log(H.red("  Upload credentials are required for S3 access.")),console.log(H.gray("  Re-run the command to retry.")),process.exit(1)}Q=N("Configuring S3 remote...").start();let A0=await w4(J,{name:"nemar-s3",bucket:R.s3.bucket,prefix:`${O.dataset_id}/objects`,region:R.s3.region,publicUrl:O.s3_config.public_url},nD(R.credentials));if(!A0.success)Q.fail(`Failed to configure S3 remote: ${A0.error}`),console.log(H.gray("  Re-run the command to retry.")),process.exit(1);Q.succeed("S3 remote configured"),Q=N("Tracking data files with git-annex...").start();let d=await U9(J);if(!d.success)Q.fail(`Failed to track data files: ${d.error}`),process.exit(1);Q.succeed("Data files tracked by git-annex"),Q=N(`Uploading ${C.length} data files to S3...`).start();let p=await T4(J,"nemar-s3",Number.parseInt(F.jobs,10),nD(R.credentials));if(await A1(J),!p.success)Q.fail(`S3 upload failed: ${p.error}`),console.log(H.yellow("Re-run the same command to resume uploading.")),process.exit(1);for(let W0 of C)Yg(L,W0.path);p1(J,L),Q.succeed(`Uploaded ${p.filesCopied} data files to S3`)}else console.log(H.gray("No data files to upload to S3"));AF(L,"s3_upload"),p1(J,L)}else console.log(H.gray("  S3 upload already completed (skipping)"));if(!LF(L,"metadata_write")){if(q)try{let R=$D(J,".nemar"),A0=$D(R,"metadata.json");if(!JD(A0)){if(!JD(R))Rg(R,{recursive:!0});k4(A0,JSON.stringify(q,null,2))}let d=$D(J,".bidsignore"),p="";if(JD(d))p=L8(d,"utf-8");if(!p.includes(".nemar/")){let W0=p?`${p.trimEnd()}
+`;k4(R,d)}}catch(R){console.log(H.yellow(`  Warning: Could not update .gitignore: ${p0(R)}`))}Q=N("Configuring GitHub remote...").start();let t=await f6(J,O.ssh_url);if(!t.success)Q.fail("Failed to configure GitHub remote"),console.log(H.red(`  ${t.error}`)),process.exit(1);if(Q.succeed("GitHub remote configured"),!await zf(J,{yes:F.yes}))process.exit(1);if(!L)L=Qg(J,O.dataset_id,M);else{for(let R of M)if(!L.files[R.path])L.files[R.path]={status:"pending",size:R.size,updated_at:new Date().toISOString()};p1(J,L)}if(!LF(L,"s3_upload")){if(C.length>0){Q=N("Requesting upload credentials...").start();let R;try{R=await R4(O.dataset_id),Q.succeed("Upload credentials received (2h expiry)")}catch(W0){Q.fail(`Could not get upload credentials: ${p0(W0)}`),console.log(H.red("  Upload credentials are required for S3 access.")),console.log(H.dim("  Re-run the command to retry.")),process.exit(1)}Q=N("Configuring S3 remote...").start();let A0=await w4(J,{name:"nemar-s3",bucket:R.s3.bucket,prefix:`${O.dataset_id}/objects`,region:R.s3.region,publicUrl:O.s3_config.public_url},nD(R.credentials));if(!A0.success)Q.fail(`Failed to configure S3 remote: ${A0.error}`),console.log(H.dim("  Re-run the command to retry.")),process.exit(1);Q.succeed("S3 remote configured"),Q=N("Tracking data files with git-annex...").start();let d=await U9(J);if(!d.success)Q.fail(`Failed to track data files: ${d.error}`),process.exit(1);Q.succeed("Data files tracked by git-annex"),Q=N(`Uploading ${C.length} data files to S3...`).start();let p=await T4(J,"nemar-s3",Number.parseInt(F.jobs,10),nD(R.credentials));if(await A1(J),!p.success)Q.fail(`S3 upload failed: ${p.error}`),console.log(H.yellow("Re-run the same command to resume uploading.")),process.exit(1);for(let W0 of C)Yg(L,W0.path);p1(J,L),Q.succeed(`Uploaded ${p.filesCopied} data files to S3`)}else console.log(H.dim("No data files to upload to S3"));AF(L,"s3_upload"),p1(J,L)}else console.log(H.dim("  S3 upload already completed (skipping)"));if(!LF(L,"metadata_write")){if(q)try{let R=$D(J,".nemar"),A0=$D(R,"metadata.json");if(!JD(A0)){if(!JD(R))Rg(R,{recursive:!0});k4(A0,JSON.stringify(q,null,2))}let d=$D(J,".bidsignore"),p="";if(JD(d))p=L8(d,"utf-8");if(!p.includes(".nemar/")){let W0=p?`${p.trimEnd()}
 .nemar/
 `:`.nemar/
-`;k4(d,W0)}console.log(H.gray("  Updated .bidsignore for NEMAR metadata"))}catch(R){console.log(H.yellow(`  Warning: Could not update .bidsignore: ${p0(R)}`)),console.log(H.gray("  Upload will continue without author enrichment."))}AF(L,"metadata_write"),p1(J,L)}else console.log(H.gray("  Metadata write already completed (skipping)"));if(!LF(L,"dataset_save")){Q=N("Saving dataset changes...").start();let R=await g6(J,"Initial NEMAR dataset upload",f);if(!R.success)p1(J,L),Q.fail("Failed to save dataset"),console.log(H.red(`  ${R.error}`)),console.log(),console.log(H.yellow("Re-run the same command to resume from this step.")),process.exit(1);Q.succeed("Dataset changes saved"),AF(L,"dataset_save"),p1(J,L)}else console.log(H.gray("  Dataset save already completed (skipping)"));if(!LF(L,"github_push")){Q=N("Pushing metadata to GitHub...").start();let R=await Z8(J);if(!R.success)p1(J,L),Q.fail("Failed to push to GitHub"),console.log(H.red(`  ${R.error}`)),console.log(),console.log(H.yellow("Re-run the same command to resume from this step.")),process.exit(1);if(R.warning)Q.warn("Metadata pushed to GitHub (with warning)"),console.log(H.yellow(`  ${R.warning}`));else Q.succeed("Metadata pushed to GitHub");AF(L,"github_push"),p1(J,L)}else console.log(H.gray("  GitHub push already completed (skipping)"));if(!LF(L,"ci_deploy")){Q=N("Setting up BIDS validation CI...").start();try{await EF(O.dataset_id),Q.succeed("BIDS validation CI configured")}catch(R){if(R instanceof i&&R.statusCode===403)Q.info("CI workflow will be configured by an admin");else{let A0=R instanceof Error?R.message:String(R);Q.warn(`Could not configure CI: ${A0}`),console.log(H.gray(`  An admin can add it later with: nemar admin ci add ${O.dataset_id}`))}}AF(L,"ci_deploy"),p1(J,L)}else console.log(H.gray("  CI deploy already completed (skipping)"));eJ(J),af(J),console.log(),console.log(H.green.bold("Upload complete!")),console.log(),console.log(`  Dataset ID: ${H.cyan(O.dataset_id)}`),console.log(`  GitHub: ${H.cyan(O.github_url)}`),console.log(),console.log(H.gray("To download this dataset:")),console.log(H.gray(`  nemar dataset download ${O.dataset_id}`)),console.log(),console.log(H.yellow("Note: This dataset is private. Only the owner and designated collaborators can")),console.log(H.yellow("download it, and only through the NEMAR CLI (not direct git-annex commands).")),console.log(H.yellow("After publishing, the data will be publicly available for everyone."))});DD.command("download").description("Download a dataset from NEMAR").argument("<dataset-id>","Dataset ID (e.g., nm000104)").option("-o, --output <path>","Output directory (default: ./<dataset-id>)").option("-j, --jobs <number>","Parallel download streams (default: 4)","4").option("--no-data","Download metadata only (skip large data files)").addHelpText("after",`
+`;k4(d,W0)}console.log(H.dim("  Updated .bidsignore for NEMAR metadata"))}catch(R){console.log(H.yellow(`  Warning: Could not update .bidsignore: ${p0(R)}`)),console.log(H.dim("  Upload will continue without author enrichment."))}AF(L,"metadata_write"),p1(J,L)}else console.log(H.dim("  Metadata write already completed (skipping)"));if(!LF(L,"dataset_save")){Q=N("Saving dataset changes...").start();let R=await g6(J,"Initial NEMAR dataset upload",f);if(!R.success)p1(J,L),Q.fail("Failed to save dataset"),console.log(H.red(`  ${R.error}`)),console.log(),console.log(H.yellow("Re-run the same command to resume from this step.")),process.exit(1);Q.succeed("Dataset changes saved"),AF(L,"dataset_save"),p1(J,L)}else console.log(H.dim("  Dataset save already completed (skipping)"));if(!LF(L,"github_push")){Q=N("Pushing metadata to GitHub...").start();let R=await Z8(J);if(!R.success)p1(J,L),Q.fail("Failed to push to GitHub"),console.log(H.red(`  ${R.error}`)),console.log(),console.log(H.yellow("Re-run the same command to resume from this step.")),process.exit(1);if(R.warning)Q.warn("Metadata pushed to GitHub (with warning)"),console.log(H.yellow(`  ${R.warning}`));else Q.succeed("Metadata pushed to GitHub");AF(L,"github_push"),p1(J,L)}else console.log(H.dim("  GitHub push already completed (skipping)"));if(!LF(L,"ci_deploy")){Q=N("Setting up BIDS validation CI...").start();try{await EF(O.dataset_id),Q.succeed("BIDS validation CI configured")}catch(R){if(R instanceof i&&R.statusCode===403)Q.info("CI workflow will be configured by an admin");else{let A0=R instanceof Error?R.message:String(R);Q.warn(`Could not configure CI: ${A0}`),console.log(H.dim(`  An admin can add it later with: nemar admin ci add ${O.dataset_id}`))}}AF(L,"ci_deploy"),p1(J,L)}else console.log(H.dim("  CI deploy already completed (skipping)"));eJ(J),af(J),console.log(),console.log(H.green.bold("Upload complete!")),console.log(),console.log(`  Dataset ID: ${H.cyan(O.dataset_id)}`),console.log(`  GitHub: ${H.cyan(O.github_url)}`),console.log(),console.log(H.dim("To download this dataset:")),console.log(H.dim(`  nemar dataset download ${O.dataset_id}`)),console.log(),console.log(H.yellow("Note: This dataset is private. Only the owner and designated collaborators can")),console.log(H.yellow("download it, and only through the NEMAR CLI (not direct git-annex commands).")),console.log(H.yellow("After publishing, the data will be publicly available for everyone."))});DD.command("download").description("Download a dataset from NEMAR").argument("<dataset-id>","Dataset ID (e.g., nm000104)").option("-o, --output <path>","Output directory (default: ./<dataset-id>)").option("-j, --jobs <number>","Parallel download streams (default: 4)","4").option("--no-data","Download metadata only (skip large data files)").addHelpText("after",`
 Description:
   Download a BIDS dataset from NEMAR. Uses git-annex for efficient
   data transfer with parallel streams.
@@ -545,14 +543,14 @@ Examples:
   $ nemar dataset download nm000104              # Download to ./nm000104
   $ nemar dataset download nm000104 -o ./data    # Custom output directory
   $ nemar dataset download nm000104 --no-data    # Metadata only (fast)
-  $ nemar dataset download nm000104 -j 8         # More parallel streams`).action(async(D,F)=>{await rJ("download");let $=N("Checking git-annex...").start(),J=await A9();if(!J.allPassed){$.fail("Prerequisites check failed"),console.log();for(let z of J.errors)console.log(H.red(`  - ${z}`));process.exit(1)}$.succeed(`git-annex ${J.gitAnnex.version}`),$=N(`Fetching dataset info for ${D}...`).start();let Q;try{Q=await cD(D),$.succeed(`Found dataset: ${Q.name}`)}catch(z){if($.fail("Dataset not found"),z instanceof i)console.log(H.red(`  ${z.message}`));else console.log(H.red(`  ${z.message}`));process.exit(1)}if(!Q.github_repo)console.log(H.red("Error: Dataset repository not available")),process.exit(1);let B=F.output||D,Y=$D(B);if(JD(Y))console.log(H.red(`Error: Output path already exists: ${Y}`)),console.log("Remove or rename the existing directory and try again."),process.exit(1);if(console.log(),console.log(H.bold("Download Plan:")),console.log(`  Dataset: ${Q.name} (${D})`),console.log(`  Output: ${Y}`),console.log(`  Data files: ${F.data===!1?"metadata only":"included"}`),F.data!==!1)console.log(`  Parallel jobs: ${F.jobs}`);console.log();let X=`https://github.com/${Q.github_repo}.git`;$=N("Cloning metadata from GitHub...").start();let G=await U8(X,Y);if(!G.success)$.fail("Failed to clone dataset"),console.log(H.red(`  ${G.error}`)),process.exit(1);$.succeed("Metadata cloned");let W=null;if(Q.visibility!=="public"){$=N("Requesting download credentials...").start();try{W=await gJ(D),$.succeed("Download credentials received (2h expiry)")}catch(z){$.fail("Failed to get download credentials"),console.log(H.red(`  ${z.message}`)),console.log(H.gray("Private datasets require authentication. Run 'nemar auth login' first.")),process.exit(1)}}let q=W?nD(W.credentials):void 0,K=await ZF(Y,"nemar-s3",q);if(K.enabled)console.log(H.gray("  S3 remote enabled for data downloads"));else if(!K.success)console.log(H.yellow(`  Warning: Could not enable S3 remote: ${K.error}`));if(F.data!==!1){console.log(H.bold(`Downloading data files (${F.jobs} parallel streams)...`));let z=new FW,U=await QW(Y,{jobs:Number.parseInt(F.jobs,10),credentials:q,onProgress:(A)=>z.processLine(A)});if(!U.success){if(z.finish(0),console.log(H.red(`Failed to download data files: ${U.error}`)),console.log(H.gray("The dataset was cloned but data files are not available locally.")),console.log(H.gray(`You can try again with: cd ${Y} && nemar dataset get`)),W)await A1(Y);process.exit(1)}z.finish(U.filesDownloaded||0),console.log(H.green(`Data downloaded (${U.filesDownloaded||0} files)`))}else console.log(H.gray("Skipping data files (--no-data flag)"));if(W)await A1(Y);let Z=await Wf(Y);if(console.log(),console.log(H.green.bold("Download complete!")),console.log(),console.log(`  Location: ${H.cyan(Y)}`),Z){if(console.log(`  Files: ${Z.files}`),Z.size!=="unknown")console.log(`  Size: ${Z.size}`);if(Z.missingFiles>0)console.log(H.gray(`  Missing files: ${Z.missingFiles} (use 'git annex get' to download)`))}console.log(),console.log(H.gray("To get additional data:")),console.log(H.gray(`  cd ${Y} && git annex get <path>`))});DD.command("status").description("Check status of a dataset").argument("<dataset-id>","Dataset ID (e.g., nm000104)").option("--json","Output as JSON for scripting").addHelpText("after",`
+  $ nemar dataset download nm000104 -j 8         # More parallel streams`).action(async(D,F)=>{await rJ("download");let $=N("Checking git-annex...").start(),J=await A9();if(!J.allPassed){$.fail("Prerequisites check failed"),console.log();for(let z of J.errors)console.log(H.red(`  - ${z}`));process.exit(1)}$.succeed(`git-annex ${J.gitAnnex.version}`),$=N(`Fetching dataset info for ${D}...`).start();let Q;try{Q=await cD(D),$.succeed(`Found dataset: ${Q.name}`)}catch(z){if($.fail("Dataset not found"),z instanceof i)console.log(H.red(`  ${z.message}`));else console.log(H.red(`  ${z.message}`));process.exit(1)}if(!Q.github_repo)console.log(H.red("Error: Dataset repository not available")),process.exit(1);let B=F.output||D,Y=$D(B);if(JD(Y))console.log(H.red(`Error: Output path already exists: ${Y}`)),console.log("Remove or rename the existing directory and try again."),process.exit(1);if(console.log(),console.log(H.bold("Download Plan:")),console.log(`  Dataset: ${Q.name} (${D})`),console.log(`  Output: ${Y}`),console.log(`  Data files: ${F.data===!1?"metadata only":"included"}`),F.data!==!1)console.log(`  Parallel jobs: ${F.jobs}`);console.log();let X=`https://github.com/${Q.github_repo}.git`;$=N("Cloning metadata from GitHub...").start();let G=await U8(X,Y);if(!G.success)$.fail("Failed to clone dataset"),console.log(H.red(`  ${G.error}`)),process.exit(1);$.succeed("Metadata cloned");let W=null;if(Q.visibility!=="public"){$=N("Requesting download credentials...").start();try{W=await gJ(D),$.succeed("Download credentials received (2h expiry)")}catch(z){$.fail("Failed to get download credentials"),console.log(H.red(`  ${z.message}`)),console.log(H.dim("Private datasets require authentication. Run 'nemar auth login' first.")),process.exit(1)}}let q=W?nD(W.credentials):void 0,K=await ZF(Y,"nemar-s3",q);if(K.enabled)console.log(H.dim("  S3 remote enabled for data downloads"));else if(!K.success)console.log(H.yellow(`  Warning: Could not enable S3 remote: ${K.error}`));if(F.data!==!1){console.log(H.bold(`Downloading data files (${F.jobs} parallel streams)...`));let z=new FW,U=await QW(Y,{jobs:Number.parseInt(F.jobs,10),credentials:q,onProgress:(A)=>z.processLine(A)});if(!U.success){if(z.finish(0),console.log(H.red(`Failed to download data files: ${U.error}`)),console.log(H.dim("The dataset was cloned but data files are not available locally.")),console.log(H.dim(`You can try again with: cd ${Y} && nemar dataset get`)),W)await A1(Y);process.exit(1)}z.finish(U.filesDownloaded||0),console.log(H.green(`Data downloaded (${U.filesDownloaded||0} files)`))}else console.log(H.dim("Skipping data files (--no-data flag)"));if(W)await A1(Y);let Z=await Wf(Y);if(console.log(),console.log(H.green.bold("Download complete!")),console.log(),console.log(`  Location: ${H.cyan(Y)}`),Z){if(console.log(`  Files: ${Z.files}`),Z.size!=="unknown")console.log(`  Size: ${Z.size}`);if(Z.missingFiles>0)console.log(H.dim(`  Missing files: ${Z.missingFiles} (use 'git annex get' to download)`))}console.log(),console.log(H.dim("To get additional data:")),console.log(H.dim(`  cd ${Y} && git annex get <path>`))});DD.command("status").description("Check status of a dataset").argument("<dataset-id>","Dataset ID (e.g., nm000104)").option("--json","Output as JSON for scripting").addHelpText("after",`
 Description:
   Show detailed information about a NEMAR dataset including owner,
   creation date, GitHub repository, and DOI information.
 Examples:
   $ nemar dataset status nm000104
-  $ nemar dataset status nm000104 --json | jq '.concept_doi'`).action(async(D,F)=>{let $=N(`Fetching dataset info for ${D}...`).start(),J;try{J=await cD(D),$.stop()}catch(Q){if($.fail("Dataset not found"),Q instanceof i)console.log(H.red(`  ${Q.message}`));else console.log(H.red(`  ${Q.message}`));process.exit(1)}if(F.json){console.log(JSON.stringify(J,null,2));return}if(console.log(),console.log(H.bold(`Dataset: ${J.dataset_id}`)),console.log(),console.log(`  Name:        ${J.name}`),console.log(`  Owner:       ${J.owner_username}`),console.log(`  Status:      ${wg(J.status)}`),console.log(`  Created:     ${new Date(J.created_at).toLocaleDateString()}`),J.description)console.log(`  Description: ${J.description}`);if(J.github_repo)console.log(`  GitHub:      https://github.com/${J.github_repo}`);if(J.concept_doi)console.log(`  DOI:         https://doi.org/${J.concept_doi}`);console.log(),console.log(H.gray("To download this dataset:")),console.log(H.gray(`  nemar dataset download ${D}`))});function wg(D){switch(D.toLowerCase()){case"published":return H.green(D);case"active":return H.blue(D);case"archived":return H.gray(D);case"pending":return H.yellow(D);default:return D}}DD.command("list").description("List publicly available datasets on NEMAR").option("--mine","List only your datasets (both private and public)").option("--json","Output as JSON for scripting").option("--limit <n>","Limit number of results (default: 50)","50").addHelpText("after",`
+  $ nemar dataset status nm000104 --json | jq '.concept_doi'`).action(async(D,F)=>{let $=N(`Fetching dataset info for ${D}...`).start(),J;try{J=await cD(D),$.stop()}catch(Q){if($.fail("Dataset not found"),Q instanceof i)console.log(H.red(`  ${Q.message}`));else console.log(H.red(`  ${Q.message}`));process.exit(1)}if(F.json){console.log(JSON.stringify(J,null,2));return}if(console.log(),console.log(H.bold(`Dataset: ${J.dataset_id}`)),console.log(),console.log(`  Name:        ${J.name}`),console.log(`  Owner:       ${J.owner_username}`),console.log(`  Status:      ${wg(J.status)}`),console.log(`  Created:     ${new Date(J.created_at).toLocaleDateString()}`),J.description)console.log(`  Description: ${J.description}`);if(J.github_repo)console.log(`  GitHub:      https://github.com/${J.github_repo}`);if(J.concept_doi)console.log(`  DOI:         https://doi.org/${J.concept_doi}`);console.log(),console.log(H.dim("To download this dataset:")),console.log(H.dim(`  nemar dataset download ${D}`))});function wg(D){switch(D.toLowerCase()){case"published":return H.green(D);case"active":return H.blue(D);case"archived":return H.dim(D);case"pending":return H.yellow(D);default:return D}}DD.command("list").description("List publicly available datasets on NEMAR").option("--mine","List only your datasets (both private and public)").option("--json","Output as JSON for scripting").option("--limit <n>","Limit number of results (default: 50)","50").addHelpText("after",`
 Description:
   By default, lists only PUBLIC datasets on NEMAR that anyone can access.
@@ -573,7 +571,7 @@ Examples:
   $ nemar dataset list                   # List public datasets only
   $ nemar dataset list --mine            # List YOUR datasets (private + public)
   $ nemar dataset list --json            # JSON output for scripting
-  $ nemar dataset list --limit 10        # Show only 10 datasets`).action(async(D)=>{if(D.mine&&!v0())console.log(H.red("Error: Not authenticated")),console.log("Run 'nemar auth login' to see your datasets"),process.exit(1);let F=N("Fetching datasets...").start(),$;try{$=await I_(!!D.mine),F.stop()}catch(q){if(F.fail("Failed to fetch datasets"),q instanceof i)console.log(H.red(`  ${q.message}`));else console.log(H.red(`  ${q.message}`));process.exit(1)}let J=$.datasets;if(D.mine){let K=YD().username;J=J.filter((Z)=>Z.owner_username===K)}let Q=Number.parseInt(D.limit,10);if(J.length>Q)J=J.slice(0,Q);if(D.json){console.log(JSON.stringify(J,null,2));return}if(J.length===0){if(console.log(),D.mine)console.log(H.yellow("You don't have any datasets yet.")),console.log(H.gray("Create one with: nemar dataset upload <path>"));else console.log(H.yellow("No datasets found."));return}console.log(),console.log(H.bold(`Datasets (${J.length}${$.count>J.length?` of ${$.count}`:""}):`)),console.log();let B=Math.max(10,...J.map((q)=>q.dataset_id.length)),Y=Math.min(30,Math.max(10,...J.map((q)=>q.name.length))),X=Math.max(8,...J.map((q)=>q.owner_username.length)),G=10,W=["ID".padEnd(B),"Name".padEnd(Y),"Owner".padEnd(X),"Visibility".padEnd(G),"Status"].join("  ");console.log(H.gray(W)),console.log(H.gray("-".repeat(W.length)));for(let q of J){let K=q.name.length>Y?`${q.name.substring(0,Y-3)}...`:q.name,Z=q.visibility==="public"?H.green("public"):H.yellow("private"),z=[H.cyan(q.dataset_id.padEnd(B)),K.padEnd(Y),q.owner_username.padEnd(X),Z.padEnd(G+(Z.length-q.visibility.length)),wg(q.status)].join("  ");console.log(z)}console.log(),console.log(H.gray("For details: nemar dataset status <dataset-id>"))});DD.command("release").description("Create a version bump PR for a dataset").argument("<dataset-id>","Dataset ID (e.g., nm000104)").option("--type <type>","Bump type: patch, minor, or major").option("--version <version>","Explicit version (e.g., 2.0.0)").option("--dir <path>","Use existing local clone instead of cloning").option("--monitor","Watch CI checks and offer to merge").option(I0,S0).addHelpText("after",`
+  $ nemar dataset list --limit 10        # Show only 10 datasets`).action(async(D)=>{if(D.mine&&!v0())console.log(H.red("Error: Not authenticated")),console.log("Run 'nemar auth login' to see your datasets"),process.exit(1);let F=N("Fetching datasets...").start(),$;try{$=await I_(!!D.mine),F.stop()}catch(q){if(F.fail("Failed to fetch datasets"),q instanceof i)console.log(H.red(`  ${q.message}`));else console.log(H.red(`  ${q.message}`));process.exit(1)}let J=$.datasets;if(D.mine){let K=YD().username;J=J.filter((Z)=>Z.owner_username===K)}let Q=Number.parseInt(D.limit,10);if(J.length>Q)J=J.slice(0,Q);if(D.json){console.log(JSON.stringify(J,null,2));return}if(J.length===0){if(console.log(),D.mine)console.log(H.yellow("You don't have any datasets yet.")),console.log(H.dim("Create one with: nemar dataset upload <path>"));else console.log(H.yellow("No datasets found."));return}console.log(),console.log(H.bold(`Datasets (${J.length}${$.count>J.length?` of ${$.count}`:""}):`)),console.log();let B=Math.max(10,...J.map((q)=>q.dataset_id.length)),Y=Math.min(30,Math.max(10,...J.map((q)=>q.name.length))),X=Math.max(8,...J.map((q)=>q.owner_username.length)),G=10,W=["ID".padEnd(B),"Name".padEnd(Y),"Owner".padEnd(X),"Visibility".padEnd(G),"Status"].join("  ");console.log(H.dim(W)),console.log(H.dim("-".repeat(W.length)));for(let q of J){let K=q.name.length>Y?`${q.name.substring(0,Y-3)}...`:q.name,Z=q.visibility==="public"?H.green("public"):H.yellow("private"),z=[H.cyan(q.dataset_id.padEnd(B)),K.padEnd(Y),q.owner_username.padEnd(X),Z.padEnd(G+(Z.length-q.visibility.length)),wg(q.status)].join("  ");console.log(z)}console.log(),console.log(H.dim("For details: nemar dataset status <dataset-id>"))});DD.command("release").description("Create a version bump PR for a dataset").argument("<dataset-id>","Dataset ID (e.g., nm000104)").option("--type <type>","Bump type: patch, minor, or major").option("--version <version>","Explicit version (e.g., 2.0.0)").option("--dir <path>","Use existing local clone instead of cloning").option("--monitor","Watch CI checks and offer to merge").option(I0,S0).addHelpText("after",`
 Description:
   Create a pull request that bumps the dataset version in
   dataset_description.json. The PR triggers CI checks (BIDS validation,
@@ -583,15 +581,15 @@ Description:
 Examples:
   $ nemar dataset release nm000104 --type patch
   $ nemar dataset release nm000104 --version 2.0.0
-  $ nemar dataset release nm000104                   # interactive prompt`).action(async(D,F)=>{if(!v0())console.log(H.red("Error: Not authenticated")),console.log("Run 'nemar auth login' first"),process.exit(1);if(await QD({cmd:["git","--version"],stdout:"pipe",stderr:"pipe"}).exited!==0)console.log(H.red("Error: git is not installed")),process.exit(1);if(await QD({cmd:["gh","--version"],stdout:"pipe",stderr:"pipe"}).exited!==0)console.log(H.red("Error: GitHub CLI (gh) is not installed")),console.log("  Install: brew install gh (or see https://cli.github.com)"),process.exit(1);let Q=N("Fetching dataset info...").start(),B;try{B=await cD(D),Q.succeed(`Dataset: ${B.name||D}`)}catch(T){if(T instanceof i)Q.fail(T.message);else Q.fail("Failed to fetch dataset");process.exit(1)}if(!B.github_repo)console.log(H.red("Error: Dataset has no GitHub repository")),process.exit(1);let Y;try{let T=await S_(D);if(Y=T.current_version,console.log(`  Current version: ${H.cyan(Y)}`),T.versions.length>0){console.log(`  Version DOIs: ${T.versions.length}`);for(let f of T.versions.slice(0,3))console.log(`    ${f.version} - ${H.gray(f.doi)}`);if(T.versions.length>3)console.log(H.gray(`    ... and ${T.versions.length-3} more`))}}catch(T){let f=T instanceof i?`${T.statusCode}: ${T.message}`:String(T);console.log(H.red(`Error: Could not fetch version history (${f})`)),console.log("  Cannot determine current version. Ensure the backend is reachable."),process.exit(1)}let X;if(F.version){if(!wW(F.version))console.log(H.red(`Error: Invalid version: ${F.version}`)),console.log("  Expected format: X.Y.Z (e.g., 2.0.0)"),process.exit(1);X=F.version.replace(/^v/,"")}else if(F.type){let T=F.type;if(!["patch","minor","major"].includes(T))console.log(H.red(`Error: Invalid bump type: ${F.type}`)),console.log("  Expected: patch, minor, or major"),process.exit(1);X=S4(Y,T)}else{if(!tJ(Y))console.log(H.red(`Error: Cannot parse current version: ${Y}`)),process.exit(1);let f=[{name:`patch  ${Y} -> ${S4(Y,"patch")}`,value:"patch"},{name:`minor  ${Y} -> ${S4(Y,"minor")}`,value:"minor"},{name:`major  ${Y} -> ${S4(Y,"major")}`,value:"major"},{name:"custom version",value:"custom"}],{bumpType:n}=await B0.prompt([{type:"list",name:"bumpType",message:"Select version bump type:",choices:f}]);if(n==="custom"){let{customVersion:s}=await B0.prompt([{type:"input",name:"customVersion",message:"Enter version (X.Y.Z):",validate:(h)=>wW(h)||"Invalid format. Use X.Y.Z (e.g., 2.0.0)"}]);X=s.replace(/^v/,"")}else X=S4(Y,n)}if(console.log(),console.log(`  ${H.bold("Version bump:")} ${Y} -> ${H.green(X)}`),await y0(`Create release PR for ${D} v${X}?`,{yes:F.yes})!=="confirmed"){console.log("Cancelled.");return}let W,q=!0;if(F.dir){if(!JD(F.dir))console.log(H.red(`Error: Directory not found: ${F.dir}`)),process.exit(1);W=$D(F.dir),q=!1}else W=SE0(P9(kE0(),`nemar-release-${D}-`));if(q){let T=`https://github.com/${B.github_repo}.git`,f=N("Cloning dataset...").start(),n=await U8(T,W);if(!n.success)f.fail(`Clone failed: ${n.error}`),process.exit(1);f.succeed("Cloned dataset")}let K=`release/v${X}`,Z=N("Creating release branch...").start(),z=QD({cmd:["git","checkout","-b",K],cwd:W,stdout:"pipe",stderr:"pipe"});if(await z.exited!==0){let T=await new Response(z.stderr).text();Z.fail(`Failed to create branch: ${T.trim()}`),process.exit(1)}Z.succeed(`Created branch: ${K}`);let U=P9(W,"dataset_description.json");if(!JD(U))console.log(H.red("Error: dataset_description.json not found in repo")),process.exit(1);let A;try{A=JSON.parse(L8(U,"utf-8"))}catch(T){if(T instanceof SyntaxError)console.log(H.red("Error: dataset_description.json contains invalid JSON"));else console.log(H.red(`Error: Could not read dataset_description.json: ${T}`));process.exit(1)}A.Version=X,k4(U,`${JSON.stringify(A,null,2)}
+  $ nemar dataset release nm000104                   # interactive prompt`).action(async(D,F)=>{if(!v0())console.log(H.red("Error: Not authenticated")),console.log("Run 'nemar auth login' first"),process.exit(1);if(await QD({cmd:["git","--version"],stdout:"pipe",stderr:"pipe"}).exited!==0)console.log(H.red("Error: git is not installed")),process.exit(1);if(await QD({cmd:["gh","--version"],stdout:"pipe",stderr:"pipe"}).exited!==0)console.log(H.red("Error: GitHub CLI (gh) is not installed")),console.log("  Install: brew install gh (or see https://cli.github.com)"),process.exit(1);let Q=N("Fetching dataset info...").start(),B;try{B=await cD(D),Q.succeed(`Dataset: ${B.name||D}`)}catch(T){if(T instanceof i)Q.fail(T.message);else Q.fail("Failed to fetch dataset");process.exit(1)}if(!B.github_repo)console.log(H.red("Error: Dataset has no GitHub repository")),process.exit(1);let Y;try{let T=await S_(D);if(Y=T.current_version,console.log(`  Current version: ${H.cyan(Y)}`),T.versions.length>0){console.log(`  Version DOIs: ${T.versions.length}`);for(let f of T.versions.slice(0,3))console.log(`    ${f.version} - ${H.dim(f.doi)}`);if(T.versions.length>3)console.log(H.dim(`    ... and ${T.versions.length-3} more`))}}catch(T){let f=T instanceof i?`${T.statusCode}: ${T.message}`:String(T);console.log(H.red(`Error: Could not fetch version history (${f})`)),console.log("  Cannot determine current version. Ensure the backend is reachable."),process.exit(1)}let X;if(F.version){if(!wW(F.version))console.log(H.red(`Error: Invalid version: ${F.version}`)),console.log("  Expected format: X.Y.Z (e.g., 2.0.0)"),process.exit(1);X=F.version.replace(/^v/,"")}else if(F.type){let T=F.type;if(!["patch","minor","major"].includes(T))console.log(H.red(`Error: Invalid bump type: ${F.type}`)),console.log("  Expected: patch, minor, or major"),process.exit(1);X=S4(Y,T)}else{if(!tJ(Y))console.log(H.red(`Error: Cannot parse current version: ${Y}`)),process.exit(1);let f=[{name:`patch  ${Y} -> ${S4(Y,"patch")}`,value:"patch"},{name:`minor  ${Y} -> ${S4(Y,"minor")}`,value:"minor"},{name:`major  ${Y} -> ${S4(Y,"major")}`,value:"major"},{name:"custom version",value:"custom"}],{bumpType:n}=await B0.prompt([{type:"list",name:"bumpType",message:"Select version bump type:",choices:f}]);if(n==="custom"){let{customVersion:s}=await B0.prompt([{type:"input",name:"customVersion",message:"Enter version (X.Y.Z):",validate:(h)=>wW(h)||"Invalid format. Use X.Y.Z (e.g., 2.0.0)"}]);X=s.replace(/^v/,"")}else X=S4(Y,n)}if(console.log(),console.log(`  ${H.bold("Version bump:")} ${Y} -> ${H.green(X)}`),await y0(`Create release PR for ${D} v${X}?`,{yes:F.yes})!=="confirmed"){console.log("Cancelled.");return}let W,q=!0;if(F.dir){if(!JD(F.dir))console.log(H.red(`Error: Directory not found: ${F.dir}`)),process.exit(1);W=$D(F.dir),q=!1}else W=SE0(P9(kE0(),`nemar-release-${D}-`));if(q){let T=`https://github.com/${B.github_repo}.git`,f=N("Cloning dataset...").start(),n=await U8(T,W);if(!n.success)f.fail(`Clone failed: ${n.error}`),process.exit(1);f.succeed("Cloned dataset")}let K=`release/v${X}`,Z=N("Creating release branch...").start(),z=QD({cmd:["git","checkout","-b",K],cwd:W,stdout:"pipe",stderr:"pipe"});if(await z.exited!==0){let T=await new Response(z.stderr).text();Z.fail(`Failed to create branch: ${T.trim()}`),process.exit(1)}Z.succeed(`Created branch: ${K}`);let U=P9(W,"dataset_description.json");if(!JD(U))console.log(H.red("Error: dataset_description.json not found in repo")),process.exit(1);let A;try{A=JSON.parse(L8(U,"utf-8"))}catch(T){if(T instanceof SyntaxError)console.log(H.red("Error: dataset_description.json contains invalid JSON"));else console.log(H.red(`Error: Could not read dataset_description.json: ${T}`));process.exit(1)}A.Version=X,k4(U,`${JSON.stringify(A,null,2)}
 `);let M=N("Committing version bump...").start(),L=QD({cmd:["git","add","dataset_description.json"],cwd:W,stdout:"pipe",stderr:"pipe"});if(await L.exited!==0){let T=await new Response(L.stderr).text();M.fail(`Failed to stage changes: ${T.trim()}`),process.exit(1)}let C=QD({cmd:["git","commit","-m",`Bump version to ${X}`],cwd:W,stdout:"pipe",stderr:"pipe"});if(await C.exited!==0){let T=await new Response(C.stderr).text();M.fail(`Commit failed: ${T.trim()}`),process.exit(1)}M.succeed("Committed version bump");let O=N("Pushing branch...").start(),y=await L9(W,K);if(!y.success)O.fail(`Push failed: ${y.error}`),process.exit(1);O.succeed("Pushed branch");let w=!1,I=N("Creating pull request...").start();try{let T=`Release v${X}`,f=`## Version Bump
 Bumps ${D} from ${Y} to ${X}.
 On merge, CI will:
 - Tag the release (v${X})
-- Publish a version DOI (if concept DOI exists)`,n=QD({cmd:["gh","pr","create","--repo",B.github_repo,"--head",K,"--base","main","--title",T,"--body",f],cwd:W,stdout:"pipe",stderr:"pipe"}),s=(await new Response(n.stdout).text()).trim();if(await n.exited!==0){let h=await new Response(n.stderr).text();throw Error(h.trim()||"gh pr create failed")}w=!0,I.succeed("Created pull request"),console.log(),console.log(`  ${H.cyan("PR:")} ${s}`)}catch(T){I.fail("Failed to create PR");let f=T instanceof Error?T.message:String(T);if(console.log(H.red(`  ${f}`)),f.includes("not found")||f.includes("command not found"))console.log(H.yellow("  Install: brew install gh"));else if(f.includes("auth")||f.includes("401"))console.log(H.yellow("  Run: gh auth login"));console.log(H.gray(`  Branch ${K} has been pushed. Create the PR manually.`))}if(F.monitor&&w){console.log(),console.log(H.gray("Monitoring CI checks...")),console.log(H.gray("  Press Ctrl+C to stop monitoring"));let T=0,f=60;while(T<f){await new Promise((t)=>setTimeout(t,1e4)),T++;let n=QD({cmd:["gh","pr","checks","--repo",B.github_repo,K],cwd:W,stdout:"pipe",stderr:"pipe"}),s=await new Response(n.stdout).text();if(await n.exited===0){if(console.log(H.green("  All checks passed!")),await y0("Merge the PR?",{yes:F.yes})==="confirmed"){let t0=QD({cmd:["gh","pr","merge","--repo",B.github_repo,K,"--squash","--delete-branch"],cwd:W,stdout:"pipe",stderr:"pipe"});if(await t0.exited===0)console.log(H.green("  PR merged successfully!"));else{let A0=await new Response(t0.stderr).text();console.log(H.red(`  Merge failed: ${A0.trim()}`))}}break}if(s.includes("fail")||s.includes("X")){console.log(H.red("  Some checks failed:")),console.log(s);break}process.stdout.write(H.gray("."))}if(T>=f)console.log(H.yellow(`
-  Timed out waiting for checks.`))}if(q)console.log(),console.log(H.gray(`Working directory: ${W}`)),console.log(H.gray("You can delete this directory after the PR is merged."))});DD.command("update").description("Push local changes to a dataset via PR").argument("[path]","Path to local dataset clone (default: current directory)").option("--bump <type>","Version bump type: patch, minor, or major","patch").option("--branch <name>","Custom branch name").option("-m, --message <msg>","Commit message").option("--monitor","Watch CI checks and offer to merge").option(I0,S0).addHelpText("after",`
+- Publish a version DOI (if concept DOI exists)`,n=QD({cmd:["gh","pr","create","--repo",B.github_repo,"--head",K,"--base","main","--title",T,"--body",f],cwd:W,stdout:"pipe",stderr:"pipe"}),s=(await new Response(n.stdout).text()).trim();if(await n.exited!==0){let h=await new Response(n.stderr).text();throw Error(h.trim()||"gh pr create failed")}w=!0,I.succeed("Created pull request"),console.log(),console.log(`  ${H.cyan("PR:")} ${s}`)}catch(T){I.fail("Failed to create PR");let f=T instanceof Error?T.message:String(T);if(console.log(H.red(`  ${f}`)),f.includes("not found")||f.includes("command not found"))console.log(H.yellow("  Install: brew install gh"));else if(f.includes("auth")||f.includes("401"))console.log(H.yellow("  Run: gh auth login"));console.log(H.dim(`  Branch ${K} has been pushed. Create the PR manually.`))}if(F.monitor&&w){console.log(),console.log(H.dim("Monitoring CI checks...")),console.log(H.dim("  Press Ctrl+C to stop monitoring"));let T=0,f=60;while(T<f){await new Promise((t)=>setTimeout(t,1e4)),T++;let n=QD({cmd:["gh","pr","checks","--repo",B.github_repo,K],cwd:W,stdout:"pipe",stderr:"pipe"}),s=await new Response(n.stdout).text();if(await n.exited===0){if(console.log(H.green("  All checks passed!")),await y0("Merge the PR?",{yes:F.yes})==="confirmed"){let t0=QD({cmd:["gh","pr","merge","--repo",B.github_repo,K,"--squash","--delete-branch"],cwd:W,stdout:"pipe",stderr:"pipe"});if(await t0.exited===0)console.log(H.green("  PR merged successfully!"));else{let A0=await new Response(t0.stderr).text();console.log(H.red(`  Merge failed: ${A0.trim()}`))}}break}if(s.includes("fail")||s.includes("X")){console.log(H.red("  Some checks failed:")),console.log(s);break}process.stdout.write(H.dim("."))}if(T>=f)console.log(H.yellow(`
+  Timed out waiting for checks.`))}if(q)console.log(),console.log(H.dim(`Working directory: ${W}`)),console.log(H.dim("You can delete this directory after the PR is merged."))});DD.command("update").description("Push local changes to a dataset via PR").argument("[path]","Path to local dataset clone (default: current directory)").option("--bump <type>","Version bump type: patch, minor, or major","patch").option("--branch <name>","Custom branch name").option("-m, --message <msg>","Commit message").option("--monitor","Watch CI checks and offer to merge").option(I0,S0).addHelpText("after",`
 Description:
   Push local changes (metadata or data files) to a dataset via a pull
   request. Automatically bumps the version, commits, pushes, and creates
@@ -608,7 +606,7 @@ Examples:
   $ cd nm000104 && nemar dataset update
   $ nemar dataset update ./nm000104 --bump minor -m "Add new subjects"
   $ nemar dataset update --branch fix/metadata -m "Fix participant ages"`).action(async(D,F)=>{if(!v0())console.log(H.red("Error: Not authenticated")),console.log("Run 'nemar auth login' first"),process.exit(1);if(await QD({cmd:["git","--version"],stdout:"pipe",stderr:"pipe"}).exited!==0)console.log(H.red("Error: git is not installed")),process.exit(1);if(await QD({cmd:["gh","--version"],stdout:"pipe",stderr:"pipe"}).exited!==0)console.log(H.red("Error: GitHub CLI (gh) is not installed")),console.log("  Install: brew install gh (or see https://cli.github.com)"),process.exit(1);let Q=$D(D||".");if(!JD(P9(Q,".git")))console.log(H.red("Error: Not a git repository")),console.log("  Run this from inside a dataset clone, or pass the path."),process.exit(1);let B=await UF(Q);if(!B)console.log(H.red("Error: Could not detect dataset ID from git remote")),process.exit(1);console.log(`  Dataset: ${H.cyan(B)}`);let Y=await M9(Q);if(Y!=="main"){if(console.log(H.yellow(`Warning: Currently on branch '${Y}', expected 'main'`)),await y0("Continue anyway?",{yes:F.yes})!=="confirmed"){console.log("Cancelled.");return}}let X=QD({cmd:["git","status","--porcelain"],cwd:Q,stdout:"pipe",stderr:"pipe"}),G=(await new Response(X.stdout).text()).trim();if(await X.exited!==0)console.log(H.red("Error: Failed to check git status")),process.exit(1);if(!G){console.log(H.yellow("No changes detected.")),console.log("  Make changes to the dataset files, then run this command again.");return}let W=G.split(`
-`),q=[],K=[];for(let p of W){let W0=p.substring(3).trim();if(/\.(edf|bdf|set|fdt|nwb|eeg|vhdr|vmrk|cnt|mff|gz)$/i.test(W0))q.push(W0);else K.push(W0)}if(console.log(),K.length>0){console.log(`  ${H.bold("Metadata files:")} ${K.length}`);for(let p of K.slice(0,5))console.log(`    ${p}`);if(K.length>5)console.log(H.gray(`    ... and ${K.length-5} more`))}if(q.length>0){console.log(`  ${H.bold("Data files:")} ${q.length}`);for(let p of q.slice(0,5))console.log(`    ${p}`);if(q.length>5)console.log(H.gray(`    ... and ${q.length-5} more`))}let Z=N("Fetching dataset info...").start(),z;try{z=await cD(B),Z.succeed()}catch(p){if(p instanceof i)Z.fail(p.message);else Z.fail("Failed to fetch dataset");process.exit(1)}if(!z.github_repo)console.log(H.red("Error: Dataset has no GitHub repository")),process.exit(1);let U,A=P9(Q,"dataset_description.json");if(!JD(A))console.log(H.red("Error: dataset_description.json not found")),console.log("  This file is required for BIDS datasets."),process.exit(1);try{let p=JSON.parse(L8(A,"utf-8"));if(typeof p.Version!=="string"||!p.Version)console.log(H.red("Error: No Version field in dataset_description.json")),console.log('  Set the Version field before updating (e.g., "Version": "1.0.0").'),process.exit(1);U=p.Version}catch(p){if(p instanceof SyntaxError)console.log(H.red("Error: dataset_description.json contains invalid JSON"));else console.log(H.red(`Error: Could not read dataset_description.json: ${p}`));process.exit(1)}let M=F.bump;if(!["patch","minor","major"].includes(M))console.log(H.red(`Error: Invalid bump type: ${F.bump}`)),process.exit(1);let L=S4(U,M);if(console.log(`  ${H.bold("Version bump:")} ${U} -> ${H.green(L)}`),await y0(`Create update PR for ${B}?`,{yes:F.yes})!=="confirmed"){console.log("Cancelled.");return}let O=Date.now().toString(36),y=F.branch||`update/${B}-${O}`,w=N("Creating update branch...").start(),I=QD({cmd:["git","checkout","-b",y],cwd:Q,stdout:"pipe",stderr:"pipe"});if(await I.exited!==0){let p=await new Response(I.stderr).text();w.fail(`Failed to create branch: ${p.trim()}`),process.exit(1)}w.succeed(`Created branch: ${y}`);let T=P9(Q,"dataset_description.json"),f;try{f=JSON.parse(L8(T,"utf-8"))}catch(p){if(p instanceof SyntaxError)console.log(H.red("Error: dataset_description.json contains invalid JSON"));else console.log(H.red(`Error: Could not read dataset_description.json: ${p}`));process.exit(1)}f.Version=L,k4(T,`${JSON.stringify(f,null,2)}
+`),q=[],K=[];for(let p of W){let W0=p.substring(3).trim();if(/\.(edf|bdf|set|fdt|nwb|eeg|vhdr|vmrk|cnt|mff|gz)$/i.test(W0))q.push(W0);else K.push(W0)}if(console.log(),K.length>0){console.log(`  ${H.bold("Metadata files:")} ${K.length}`);for(let p of K.slice(0,5))console.log(`    ${p}`);if(K.length>5)console.log(H.dim(`    ... and ${K.length-5} more`))}if(q.length>0){console.log(`  ${H.bold("Data files:")} ${q.length}`);for(let p of q.slice(0,5))console.log(`    ${p}`);if(q.length>5)console.log(H.dim(`    ... and ${q.length-5} more`))}let Z=N("Fetching dataset info...").start(),z;try{z=await cD(B),Z.succeed()}catch(p){if(p instanceof i)Z.fail(p.message);else Z.fail("Failed to fetch dataset");process.exit(1)}if(!z.github_repo)console.log(H.red("Error: Dataset has no GitHub repository")),process.exit(1);let U,A=P9(Q,"dataset_description.json");if(!JD(A))console.log(H.red("Error: dataset_description.json not found")),console.log("  This file is required for BIDS datasets."),process.exit(1);try{let p=JSON.parse(L8(A,"utf-8"));if(typeof p.Version!=="string"||!p.Version)console.log(H.red("Error: No Version field in dataset_description.json")),console.log('  Set the Version field before updating (e.g., "Version": "1.0.0").'),process.exit(1);U=p.Version}catch(p){if(p instanceof SyntaxError)console.log(H.red("Error: dataset_description.json contains invalid JSON"));else console.log(H.red(`Error: Could not read dataset_description.json: ${p}`));process.exit(1)}let M=F.bump;if(!["patch","minor","major"].includes(M))console.log(H.red(`Error: Invalid bump type: ${F.bump}`)),process.exit(1);let L=S4(U,M);if(console.log(`  ${H.bold("Version bump:")} ${U} -> ${H.green(L)}`),await y0(`Create update PR for ${B}?`,{yes:F.yes})!=="confirmed"){console.log("Cancelled.");return}let O=Date.now().toString(36),y=F.branch||`update/${B}-${O}`,w=N("Creating update branch...").start(),I=QD({cmd:["git","checkout","-b",y],cwd:Q,stdout:"pipe",stderr:"pipe"});if(await I.exited!==0){let p=await new Response(I.stderr).text();w.fail(`Failed to create branch: ${p.trim()}`),process.exit(1)}w.succeed(`Created branch: ${y}`);let T=P9(Q,"dataset_description.json"),f;try{f=JSON.parse(L8(T,"utf-8"))}catch(p){if(p instanceof SyntaxError)console.log(H.red("Error: dataset_description.json contains invalid JSON"));else console.log(H.red(`Error: Could not read dataset_description.json: ${p}`));process.exit(1)}f.Version=L,k4(T,`${JSON.stringify(f,null,2)}
 `);let n=N("Committing changes...").start(),s=QD({cmd:["git","add","-A"],cwd:Q,stdout:"pipe",stderr:"pipe"});if(await s.exited!==0){let p=await new Response(s.stderr).text();n.fail(`Failed to stage changes: ${p.trim()}`),process.exit(1)}let h=F.message||`Update ${B} to ${L}`,t=QD({cmd:["git","commit","-m",h],cwd:Q,stdout:"pipe",stderr:"pipe"});if(await t.exited!==0){let p=await new Response(t.stderr).text();n.fail(`Commit failed: ${p.trim()}`),process.exit(1)}if(n.succeed("Committed changes"),q.length>0)if(await QD({cmd:["git","annex","version"],cwd:Q,stdout:"pipe",stderr:"pipe"}).exited===0){let W0=N("Requesting upload credentials...").start(),w0=null;try{w0=await R4(B),W0.succeed("Upload credentials received")}catch(K0){W0.fail(`Could not get upload credentials: ${p0(K0)}`),console.log(H.yellow("  Data files will not be uploaded. Push manually after PR."))}if(w0){if((await pJ(Q)).length===0){W0=N("Configuring S3 remote...").start();let x0=await w4(Q,{name:"nemar-s3",bucket:w0.s3.bucket,prefix:`${B}/objects`,region:w0.s3.region,publicUrl:`https://${w0.s3.bucket}.s3.${w0.s3.region}.amazonaws.com`},nD(w0.credentials));if(!x0.success)W0.warn(`Failed to configure S3 remote: ${x0.error}`),console.log(H.yellow("  Data files will not be uploaded. Push manually after PR."));else W0.succeed("S3 remote configured")}if((await pJ(Q)).includes("nemar-s3")){W0=N("Uploading data files to S3...").start();let x0=await T4(Q,"nemar-s3",4,nD(w0.credentials));if(await A1(Q),!x0.success)W0.warn(`S3 upload issue: ${x0.error}`),console.log(H.yellow("  Data files may need manual upload after PR creation."));else W0.succeed(`Uploaded ${x0.filesCopied} data files to S3`)}}}else console.log(H.yellow("  git-annex not available; data files will be committed to git."));let t0=N("Pushing branch...").start(),R=await L9(Q,y);if(!R.success)t0.fail(`Push failed: ${R.error}`),process.exit(1);if(q.length>0){if(await QD({cmd:["git","push","origin","git-annex"],cwd:Q,stdout:"pipe",stderr:"pipe"}).exited!==0)console.log(H.yellow("  Warning: Failed to push git-annex branch"))}t0.succeed("Pushed branch");let A0=!1,d=N("Creating pull request...").start();try{let p=F.message?`${F.message} (v${L})`:`Update ${B} to v${L}`,W0=[...K,...q].slice(0,10).join(`
 - `),w0=`## Dataset Update
@@ -616,7 +614,7 @@ Bumps ${B} from ${U} to ${L}.
 ### Changed files
 - ${W0}${W.length>10?`
-- ... and ${W.length-10} more`:""}`,K0=QD({cmd:["gh","pr","create","--repo",z.github_repo,"--head",y,"--base","main","--title",p,"--body",w0],cwd:Q,stdout:"pipe",stderr:"pipe"}),XD=(await new Response(K0.stdout).text()).trim();if(await K0.exited!==0){let x0=await new Response(K0.stderr).text();throw Error(x0.trim()||"gh pr create failed")}A0=!0,d.succeed("Created pull request"),console.log(),console.log(`  ${H.cyan("PR:")} ${XD}`)}catch(p){d.fail("Failed to create PR");let W0=p instanceof Error?p.message:String(p);console.log(H.red(`  ${W0}`)),console.log(H.gray(`  Branch ${y} has been pushed. Create the PR manually.`))}if(F.monitor&&A0){console.log(),console.log(H.gray("Monitoring CI checks..."));let p=0,W0=60;while(p<W0){await new Promise((x0)=>setTimeout(x0,1e4)),p++;let w0=QD({cmd:["gh","pr","checks","--repo",z.github_repo,y],cwd:Q,stdout:"pipe",stderr:"pipe"}),K0=await new Response(w0.stdout).text();if(await w0.exited===0){if(console.log(H.green("  All checks passed!")),await y0("Merge the PR?",{yes:F.yes})==="confirmed"){let $1=QD({cmd:["gh","pr","merge","--repo",z.github_repo,y,"--squash","--delete-branch"],cwd:Q,stdout:"pipe",stderr:"pipe"});if(await $1.exited===0)console.log(H.green("  PR merged successfully!"));else{let GD=await new Response($1.stderr).text();console.log(H.red(`  Merge failed: ${GD.trim()}`))}}break}if(K0.includes("fail")||K0.includes("X")){console.log(H.red("  Some checks failed:")),console.log(K0);break}process.stdout.write(H.gray("."))}if(p>=W0)console.log(H.yellow(`
+- ... and ${W.length-10} more`:""}`,K0=QD({cmd:["gh","pr","create","--repo",z.github_repo,"--head",y,"--base","main","--title",p,"--body",w0],cwd:Q,stdout:"pipe",stderr:"pipe"}),XD=(await new Response(K0.stdout).text()).trim();if(await K0.exited!==0){let x0=await new Response(K0.stderr).text();throw Error(x0.trim()||"gh pr create failed")}A0=!0,d.succeed("Created pull request"),console.log(),console.log(`  ${H.cyan("PR:")} ${XD}`)}catch(p){d.fail("Failed to create PR");let W0=p instanceof Error?p.message:String(p);console.log(H.red(`  ${W0}`)),console.log(H.dim(`  Branch ${y} has been pushed. Create the PR manually.`))}if(F.monitor&&A0){console.log(),console.log(H.dim("Monitoring CI checks..."));let p=0,W0=60;while(p<W0){await new Promise((x0)=>setTimeout(x0,1e4)),p++;let w0=QD({cmd:["gh","pr","checks","--repo",z.github_repo,y],cwd:Q,stdout:"pipe",stderr:"pipe"}),K0=await new Response(w0.stdout).text();if(await w0.exited===0){if(console.log(H.green("  All checks passed!")),await y0("Merge the PR?",{yes:F.yes})==="confirmed"){let $1=QD({cmd:["gh","pr","merge","--repo",z.github_repo,y,"--squash","--delete-branch"],cwd:Q,stdout:"pipe",stderr:"pipe"});if(await $1.exited===0)console.log(H.green("  PR merged successfully!"));else{let GD=await new Response($1.stderr).text();console.log(H.red(`  Merge failed: ${GD.trim()}`))}}break}if(K0.includes("fail")||K0.includes("X")){console.log(H.red("  Some checks failed:")),console.log(K0);break}process.stdout.write(H.dim("."))}if(p>=W0)console.log(H.yellow(`
   Timed out waiting for checks.`))}});DD.command("request-access").description("Request collaborator access to a dataset").argument("<dataset-id>","Dataset ID (e.g., nm000104)").addHelpText("after",`
 Description:
   Request access to a NEMAR dataset to push data via git-annex.
@@ -630,7 +628,7 @@ Requirements:
   - Approved user status
 Examples:
-  $ nemar dataset request-access nm000104`).action(async(D)=>{if(!v0())console.log(H.red("Error: Not authenticated")),console.log("Run 'nemar auth login' first"),process.exit(1);let F=N(`Requesting access to ${D}...`).start();try{let $=await v_(D);F.succeed($.message),console.log(),console.log(`  GitHub: https://github.com/${$.github_repo}`),console.log(),console.log(H.gray("You can now push data to this dataset via git-annex."))}catch($){if($ instanceof i)F.fail($.message);else F.fail("Failed to request access"),console.log(H.red(`  ${$.message}`));process.exit(1)}});DD.command("invite").description("Invite a user as collaborator to your dataset").argument("<username>","Username to invite").argument("<dataset-id>","Dataset ID (e.g., nm000104)").addHelpText("after",`
+  $ nemar dataset request-access nm000104`).action(async(D)=>{if(!v0())console.log(H.red("Error: Not authenticated")),console.log("Run 'nemar auth login' first"),process.exit(1);let F=N(`Requesting access to ${D}...`).start();try{let $=await v_(D);F.succeed($.message),console.log(),console.log(`  GitHub: https://github.com/${$.github_repo}`),console.log(),console.log(H.dim("You can now push data to this dataset via git-annex."))}catch($){if($ instanceof i)F.fail($.message);else F.fail("Failed to request access"),console.log(H.red(`  ${$.message}`));process.exit(1)}});DD.command("invite").description("Invite a user as collaborator to your dataset").argument("<username>","Username to invite").argument("<dataset-id>","Dataset ID (e.g., nm000104)").addHelpText("after",`
 Description:
   Invite a NEMAR user as a collaborator to your dataset.
   Only dataset owners and admins can invite collaborators.
@@ -649,7 +647,7 @@ Description:
 Examples:
   $ nemar dataset collaborators nm000104
-  $ nemar dataset collaborators nm000104 --json`).action(async(D,F)=>{if(!v0())console.log(H.red("Error: Not authenticated")),console.log("Run 'nemar auth login' first"),process.exit(1);let $=N(`Fetching collaborators for ${D}...`).start();try{let J=await x_(D);if($.stop(),F.json){console.log(JSON.stringify(J,null,2));return}if(console.log(),console.log(H.bold(`Collaborators for ${D} (${J.count}):`)),console.log(),J.collaborators.length===0){console.log(H.gray("  No collaborators yet.")),console.log(),console.log(H.gray(`Invite users with: nemar dataset invite <username> ${D}`));return}let Q=["Username","GitHub","Access","Granted"].join("  ");console.log(H.gray(`  ${Q}`)),console.log(H.gray(`  ${"-".repeat(Q.length)}`));for(let B of J.collaborators){let Y=new Date(B.granted_at).toLocaleDateString(),X=B.access_type==="invited"?"invited":"requested",G=[B.username.padEnd(10),`@${B.github_username}`.padEnd(15),X.padEnd(10),Y].join("  ");console.log(`  ${G}`)}console.log()}catch(J){if(J instanceof i)$.fail(J.message);else $.fail("Failed to fetch collaborators"),console.log(H.red(`  ${J.message}`));process.exit(1)}});var DQ=new FD("publish").description("Publication workflow management");DQ.command("request").description("Request publication of a dataset").argument("<dataset-id>","Dataset ID (e.g., nm000104)").addHelpText("after",`
+  $ nemar dataset collaborators nm000104 --json`).action(async(D,F)=>{if(!v0())console.log(H.red("Error: Not authenticated")),console.log("Run 'nemar auth login' first"),process.exit(1);let $=N(`Fetching collaborators for ${D}...`).start();try{let J=await x_(D);if($.stop(),F.json){console.log(JSON.stringify(J,null,2));return}if(console.log(),console.log(H.bold(`Collaborators for ${D} (${J.count}):`)),console.log(),J.collaborators.length===0){console.log(H.dim("  No collaborators yet.")),console.log(),console.log(H.dim(`Invite users with: nemar dataset invite <username> ${D}`));return}let Q=["Username","GitHub","Access","Granted"].join("  ");console.log(H.dim(`  ${Q}`)),console.log(H.dim(`  ${"-".repeat(Q.length)}`));for(let B of J.collaborators){let Y=new Date(B.granted_at).toLocaleDateString(),X=B.access_type==="invited"?"invited":"requested",G=[B.username.padEnd(10),`@${B.github_username}`.padEnd(15),X.padEnd(10),Y].join("  ");console.log(`  ${G}`)}console.log()}catch(J){if(J instanceof i)$.fail(J.message);else $.fail("Failed to fetch collaborators"),console.log(H.red(`  ${J.message}`));process.exit(1)}});var DQ=new FD("publish").description("Publication workflow management");DQ.command("request").description("Request publication of a dataset").argument("<dataset-id>","Dataset ID (e.g., nm000104)").addHelpText("after",`
 Description:
   Submit a publication request to make your private dataset publicly accessible.
   NEMAR admins will be notified and can approve or deny your request.
@@ -667,8 +665,8 @@ Status Flow:
 Examples:
   $ nemar dataset publish request nm000104
-  $ nemar dataset publish status nm000104     # Check request status`).action(async(D)=>{if(!v0())console.log(H.red("Error: Not authenticated")),console.log("Run 'nemar auth login' first"),process.exit(1);let F=N(`Requesting publication for ${D}...`).start();try{let $=await hJ(D);F.succeed($.message),console.log(H.gray(`
-  Admins have been notified. Use 'nemar dataset publish status' to check progress.`))}catch($){if($ instanceof i){if(F.fail($.message),console.log(H.gray(`  ${$.message}`)),$.statusCode===409)console.log(H.gray("  Use 'nemar dataset publish resend' to remind admins."));else if($.statusCode===403)console.log(H.gray("  Only the dataset owner can request publication."))}else{F.fail("Failed to request publication");let J=$ instanceof Error?$.message:String($);console.log(H.gray(`  Error details: ${J}`))}}});DQ.command("status").description("Check publication status of a dataset").argument("<dataset-id>","Dataset ID (e.g., nm000104)").addHelpText("after",`
+  $ nemar dataset publish status nm000104     # Check request status`).action(async(D)=>{if(!v0())console.log(H.red("Error: Not authenticated")),console.log("Run 'nemar auth login' first"),process.exit(1);let F=N(`Requesting publication for ${D}...`).start();try{let $=await hJ(D);F.succeed($.message),console.log(H.dim(`
+  Admins have been notified. Use 'nemar dataset publish status' to check progress.`))}catch($){if($ instanceof i){if(F.fail($.message),console.log(H.dim(`  ${$.message}`)),$.statusCode===409)console.log(H.dim("  Use 'nemar dataset publish resend' to remind admins."));else if($.statusCode===403)console.log(H.dim("  Only the dataset owner can request publication."))}else{F.fail("Failed to request publication");let J=$ instanceof Error?$.message:String($);console.log(H.dim(`  Error details: ${J}`))}}});DQ.command("status").description("Check publication status of a dataset").argument("<dataset-id>","Dataset ID (e.g., nm000104)").addHelpText("after",`
 Description:
   Check the status of your publication request and see progress through
   the approval workflow.
@@ -698,9 +696,9 @@ Steps in Approval Process:
 Examples:
   $ nemar dataset publish status nm000104`).action(async(D)=>{if(!v0())console.log(H.red("Error: Not authenticated")),console.log("Run 'nemar auth login' first"),process.exit(1);let F=N(`Checking publication status for ${D}...`).start();try{let $=await h_(D);F.stop(),console.log(`
 ${H.cyan("Publication Status:")} ${D}
-`);let Q={published:H.green,denied:H.red,approving:H.yellow}[$.status]||H.gray;if(console.log(`  Status: ${Q($.status)}`),$.requested_at)console.log(`  Requested: ${H.gray($.requested_at)}`);if($.requested_by)console.log(`  Requested by: ${H.gray($.requested_by)}`);if($.status==="denied"&&$.denied_reason)console.log(`
+`);let Q={published:H.green,denied:H.red,approving:H.yellow}[$.status]||H.dim;if(console.log(`  Status: ${Q($.status)}`),$.requested_at)console.log(`  Requested: ${H.dim($.requested_at)}`);if($.requested_by)console.log(`  Requested by: ${H.dim($.requested_by)}`);if($.status==="denied"&&$.denied_reason)console.log(`
   ${H.red("Reason:")} ${$.denied_reason}`);if($.status==="approving"){let B=["ci_check","repo_public","s3_public_read","tag_protect","doi_create","update_metadata","update_readme","create_tag","create_release","upload_to_zenodo","publish_doi","s3_lock","generate_archive","notify_user"],Y=$.steps_completed||[];console.log(`
-  Steps:`);for(let X of B){let G=Y.includes(X),W=$.current_step===X,q=G?H.green("[x]"):W?H.yellow("[>]"):H.gray("[ ]"),K=X.replace(/_/g," ");console.log(`    ${q} ${K}${W&&$.last_error?H.red(` (error: ${$.last_error})`):""}`)}}if($.status==="published"&&$.approved_at)console.log(`  Published: ${H.gray($.approved_at)}`);console.log()}catch($){if($ instanceof i)F.fail($.message),console.log(H.gray(`  ${$.message}`));else{F.fail("Failed to check publication status");let J=$ instanceof Error?$.message:String($);console.log(H.gray(`  Error details: ${J}`))}}});DQ.command("resend").description("Resend publication request notification to admins").argument("<dataset-id>","Dataset ID (e.g., nm000104)").addHelpText("after",`
+  Steps:`);for(let X of B){let G=Y.includes(X),W=$.current_step===X,q=G?H.green("[x]"):W?H.yellow("[>]"):H.dim("[ ]"),K=X.replace(/_/g," ");console.log(`    ${q} ${K}${W&&$.last_error?H.red(` (error: ${$.last_error})`):""}`)}}if($.status==="published"&&$.approved_at)console.log(`  Published: ${H.dim($.approved_at)}`);console.log()}catch($){if($ instanceof i)F.fail($.message),console.log(H.dim(`  ${$.message}`));else{F.fail("Failed to check publication status");let J=$ instanceof Error?$.message:String($);console.log(H.dim(`  Error details: ${J}`))}}});DQ.command("resend").description("Resend publication request notification to admins").argument("<dataset-id>","Dataset ID (e.g., nm000104)").addHelpText("after",`
 Description:
   Resend the publication request notification email to all NEMAR admins.
   Use this if admins haven't responded to your original request.
@@ -714,7 +712,7 @@ When to Use:
   - Your request status is still "requested"
 Examples:
-  $ nemar dataset publish resend nm000104`).action(async(D)=>{if(!v0())console.log(H.red("Error: Not authenticated")),console.log("Run 'nemar auth login' first"),process.exit(1);let F=N(`Resending notification for ${D}...`).start();try{let $=await b_(D);F.succeed($.message)}catch($){if($ instanceof i){if(F.fail($.message),console.log(H.gray(`  ${$.message}`)),$.statusCode===404)console.log(H.gray("  Publication request not found for this dataset."))}else{F.fail("Failed to resend notification");let J=$ instanceof Error?$.message:String($);console.log(H.gray(`  Error details: ${J}`))}}});DD.addCommand(DQ);DD.command("clone").description("Clone a dataset from NEMAR").argument("<dataset-id>","Dataset ID (e.g., nm000104)").option("-o, --output <path>","Output directory (default: ./<dataset-id>)").addHelpText("after",`
+  $ nemar dataset publish resend nm000104`).action(async(D)=>{if(!v0())console.log(H.red("Error: Not authenticated")),console.log("Run 'nemar auth login' first"),process.exit(1);let F=N(`Resending notification for ${D}...`).start();try{let $=await b_(D);F.succeed($.message)}catch($){if($ instanceof i){if(F.fail($.message),console.log(H.dim(`  ${$.message}`)),$.statusCode===404)console.log(H.dim("  Publication request not found for this dataset."))}else{F.fail("Failed to resend notification");let J=$ instanceof Error?$.message:String($);console.log(H.dim(`  Error details: ${J}`))}}});DD.addCommand(DQ);DD.command("clone").description("Clone a dataset from NEMAR").argument("<dataset-id>","Dataset ID (e.g., nm000104)").option("-o, --output <path>","Output directory (default: ./<dataset-id>)").addHelpText("after",`
 Description:
   Clone a NEMAR dataset repository with git-annex initialized.
   Data files are not downloaded; use 'nemar dataset get' afterward.
@@ -728,7 +726,7 @@ Requirements:
 Examples:
   $ nemar dataset clone nm000104
-  $ nemar dataset clone nm000104 -o ./my-dataset`).action(async(D,F)=>{await rJ("clone");let $=N("Checking prerequisites...").start(),J=await A9();if(!J.allPassed){$.fail("Prerequisites check failed");for(let K of J.errors)console.log(H.red(`  - ${K}`));process.exit(1)}$.succeed("Prerequisites OK"),$=N(`Resolving dataset ${D}...`).start();let Q,B;try{let K=await cD(D);if(!K.github_repo||!/^[a-zA-Z0-9_.-]+\/[a-zA-Z0-9_.-]+$/.test(K.github_repo))$.fail("Dataset has no valid GitHub repository"),console.log(H.red(`  Received: ${K.github_repo||"(empty)"}`)),process.exit(1);Q=`https://github.com/${K.github_repo}.git`,B=K.visibility,$.succeed(`Found: ${K.name}`)}catch(K){$.fail("Dataset not found");let Z=K instanceof Error?K.message:String(K);console.log(H.red(`  ${Z}`)),process.exit(1)}let Y=$D(F.output||D);if(JD(Y))console.log(H.red(`Error: Path already exists: ${Y}`)),process.exit(1);let X=null;if(B!=="public"){$=N("Requesting download credentials...").start();try{X=await gJ(D),$.succeed("Download credentials received (2h expiry)")}catch(K){$.fail("Failed to get download credentials"),console.log(H.red(`  ${K.message}`)),console.log(H.gray("Private datasets require authentication. Run 'nemar auth login' first.")),process.exit(1)}}let G=X?nD(X.credentials):void 0;$=N("Cloning dataset...").start();let W=await U8(Q,Y);if(!W.success)$.fail("Clone failed"),console.log(H.red(`  ${W.error}`)),process.exit(1);$.succeed("Dataset cloned");let q=await ZF(Y,"nemar-s3",G);if(q.enabled)console.log(H.gray("  S3 remote enabled for data downloads"));else if(!q.success)console.log(H.yellow(`  Warning: Could not enable S3 remote: ${q.error}`));if(X)await A1(Y);console.log(),console.log(`  Location: ${H.cyan(Y)}`),console.log(),console.log(H.gray("Data files are not downloaded yet. To get them:")),console.log(H.gray(`  cd ${Y}`)),console.log(H.gray("  nemar dataset get"))});DD.command("get").description("Download annexed data files for the current dataset").argument("[files...]","Specific files/paths to get (default: all)").option("-j, --jobs <number>","Parallel download streams","4").addHelpText("after",`
+  $ nemar dataset clone nm000104 -o ./my-dataset`).action(async(D,F)=>{await rJ("clone");let $=N("Checking prerequisites...").start(),J=await A9();if(!J.allPassed){$.fail("Prerequisites check failed");for(let K of J.errors)console.log(H.red(`  - ${K}`));process.exit(1)}$.succeed("Prerequisites OK"),$=N(`Resolving dataset ${D}...`).start();let Q,B;try{let K=await cD(D);if(!K.github_repo||!/^[a-zA-Z0-9_.-]+\/[a-zA-Z0-9_.-]+$/.test(K.github_repo))$.fail("Dataset has no valid GitHub repository"),console.log(H.red(`  Received: ${K.github_repo||"(empty)"}`)),process.exit(1);Q=`https://github.com/${K.github_repo}.git`,B=K.visibility,$.succeed(`Found: ${K.name}`)}catch(K){$.fail("Dataset not found");let Z=K instanceof Error?K.message:String(K);console.log(H.red(`  ${Z}`)),process.exit(1)}let Y=$D(F.output||D);if(JD(Y))console.log(H.red(`Error: Path already exists: ${Y}`)),process.exit(1);let X=null;if(B!=="public"){$=N("Requesting download credentials...").start();try{X=await gJ(D),$.succeed("Download credentials received (2h expiry)")}catch(K){$.fail("Failed to get download credentials"),console.log(H.red(`  ${K.message}`)),console.log(H.dim("Private datasets require authentication. Run 'nemar auth login' first.")),process.exit(1)}}let G=X?nD(X.credentials):void 0;$=N("Cloning dataset...").start();let W=await U8(Q,Y);if(!W.success)$.fail("Clone failed"),console.log(H.red(`  ${W.error}`)),process.exit(1);$.succeed("Dataset cloned");let q=await ZF(Y,"nemar-s3",G);if(q.enabled)console.log(H.dim("  S3 remote enabled for data downloads"));else if(!q.success)console.log(H.yellow(`  Warning: Could not enable S3 remote: ${q.error}`));if(X)await A1(Y);console.log(),console.log(`  Location: ${H.cyan(Y)}`),console.log(),console.log(H.dim("Data files are not downloaded yet. To get them:")),console.log(H.dim(`  cd ${Y}`)),console.log(H.dim("  nemar dataset get"))});DD.command("get").description("Download annexed data files for the current dataset").argument("[files...]","Specific files/paths to get (default: all)").option("-j, --jobs <number>","Parallel download streams","4").addHelpText("after",`
 Description:
   Download data files from the remote for a cloned dataset.
   Must be run inside a git-annex dataset directory.
@@ -739,7 +737,7 @@ Description:
 Examples:
   $ nemar dataset get                    # Get all files
   $ nemar dataset get sub-01/eeg/        # Get specific directory
-  $ nemar dataset get *.edf -j 8         # Get EDF files with 8 streams`).action(async(D,F)=>{let $=process.cwd();if(!await p8($))console.log(H.red("Error: Not inside a git-annex dataset directory")),console.log(H.gray("Use 'nemar dataset clone <id>' first, then cd into the dataset.")),process.exit(1);let J=Number.parseInt(F.jobs,10);if(Number.isNaN(J)||J<1)console.log(H.red("Error: --jobs must be a positive integer")),process.exit(1);let Q=null,B=await UF($);if(B){let Z=null;try{Z=await cD(B)}catch{}if(Z&&Z.visibility!=="public"){if(!v0())console.log(H.red("Error: This is a private dataset. Authentication required.")),console.log(H.gray("Run 'nemar auth login' first.")),process.exit(1);let z=N("Requesting download credentials...").start();try{Q=await gJ(B),z.succeed("Download credentials received (2h expiry)")}catch(U){z.fail("Failed to get download credentials"),console.log(H.red(`  ${U.message}`)),console.log(H.gray("Private datasets require authentication. Run 'nemar auth login' first.")),process.exit(1)}}}let Y=Q?nD(Q.credentials):void 0,X=await ZF($,"nemar-s3",Y);if(!X.success&&!X.enabled)console.log(H.yellow(`  Warning: Could not enable S3 remote: ${X.error}`));let G=D.length>0?D:void 0,W=G?`Getting ${G.length} path(s)...`:"Getting all data files...",q=N(W).start(),K=await QW($,{jobs:J,paths:G,credentials:Y});if(!K.success){if(q.fail("Failed to get data"),console.log(H.red(`  ${K.error}`)),Q)await A1($);process.exit(1)}if(Q)await A1($);if(K.filesDownloaded===0)q.succeed("All data files already present");else q.succeed(`Downloaded ${K.filesDownloaded} file(s)`)});async function Tg(D){let F=process.cwd();if(!await p8(F))console.log(H.red("Error: Not inside a git-annex dataset directory")),process.exit(1);let $=N("Saving changes...").start(),J=await g6(F,D.message);if(!J.success)$.fail("Save failed"),console.log(H.red(`  ${J.error}`)),process.exit(1);$.succeed("Changes saved")}DD.command("commit").description("Stage and commit changes in the current dataset").option("-m, --message <msg>","Commit message","Save changes").addHelpText("after",`
+  $ nemar dataset get *.edf -j 8         # Get EDF files with 8 streams`).action(async(D,F)=>{let $=process.cwd();if(!await p8($))console.log(H.red("Error: Not inside a git-annex dataset directory")),console.log(H.dim("Use 'nemar dataset clone <id>' first, then cd into the dataset.")),process.exit(1);let J=Number.parseInt(F.jobs,10);if(Number.isNaN(J)||J<1)console.log(H.red("Error: --jobs must be a positive integer")),process.exit(1);let Q=null,B=await UF($);if(B){let Z=null;try{Z=await cD(B)}catch{}if(Z&&Z.visibility!=="public"){if(!v0())console.log(H.red("Error: This is a private dataset. Authentication required.")),console.log(H.dim("Run 'nemar auth login' first.")),process.exit(1);let z=N("Requesting download credentials...").start();try{Q=await gJ(B),z.succeed("Download credentials received (2h expiry)")}catch(U){z.fail("Failed to get download credentials"),console.log(H.red(`  ${U.message}`)),console.log(H.dim("Private datasets require authentication. Run 'nemar auth login' first.")),process.exit(1)}}}let Y=Q?nD(Q.credentials):void 0,X=await ZF($,"nemar-s3",Y);if(!X.success&&!X.enabled)console.log(H.yellow(`  Warning: Could not enable S3 remote: ${X.error}`));let G=D.length>0?D:void 0,W=G?`Getting ${G.length} path(s)...`:"Getting all data files...",q=N(W).start(),K=await QW($,{jobs:J,paths:G,credentials:Y});if(!K.success){if(q.fail("Failed to get data"),console.log(H.red(`  ${K.error}`)),Q)await A1($);process.exit(1)}if(Q)await A1($);if(K.filesDownloaded===0)q.succeed("All data files already present");else q.succeed(`Downloaded ${K.filesDownloaded} file(s)`)});async function Tg(D){let F=process.cwd();if(!await p8(F))console.log(H.red("Error: Not inside a git-annex dataset directory")),process.exit(1);let $=N("Saving changes...").start(),J=await g6(F,D.message);if(!J.success)$.fail("Save failed"),console.log(H.red(`  ${J.error}`)),process.exit(1);$.succeed("Changes saved")}DD.command("commit").description("Stage and commit changes in the current dataset").option("-m, --message <msg>","Commit message","Save changes").addHelpText("after",`
 Description:
   Stage all changes (git add -A) and commit them. Large files are
   automatically handled by git-annex based on the dataset's largefiles config.
@@ -782,7 +780,7 @@ Examples:
   $ nemar dataset push
   $ nemar dataset push --no-s3      # Git only, skip S3
   $ nemar dataset push -j 8         # More parallel S3 streams
-  $ nemar dataset push --pr -t "Add new recordings"`).action(async(D)=>{let F=process.cwd();if(!await p8(F))console.log(H.red("Error: Not inside a git-annex dataset directory")),process.exit(1);let $=N("Pushing to GitHub...").start(),J=await Z8(F);if(!J.success)$.fail("Git push failed"),console.log(H.red(`  ${J.error}`)),process.exit(1);if(J.warning)$.warn("Git pushed with warning"),console.log(H.yellow(`  ${J.warning}`));else $.succeed("Pushed to GitHub");if(D.s3!==!1){let Q=await pJ(F);if(Q.length>0){let B=Q[0];if(Q.length>1)console.log(H.gray(`  Multiple S3 remotes: ${Q.join(", ")}. Using: ${B}`));let Y=Number.parseInt(D.jobs,10);if(Number.isNaN(Y)||Y<1)console.log(H.red("Error: --jobs must be a positive integer")),process.exit(1);let X=await UF(F),G=null;if(X&&v0()){$=N("Requesting upload credentials...").start();try{G=await R4(X),$.succeed("Upload credentials received")}catch(K){$.warn(`Could not get upload credentials: ${p0(K)}. Trying environment credentials.`)}}$=N(`Copying data to S3 (${B})...`).start();let W=G?nD(G.credentials):void 0,q=await T4(F,B,Y,W);if(!q.success){if($.fail("S3 push failed"),console.log(H.red(`  ${q.error}`)),!G)console.log(H.gray("  Ensure AWS_ACCESS_KEY_ID and AWS_SECRET_ACCESS_KEY are set,")),console.log(H.gray("  or log in with 'nemar auth login' for automatic credentials."));console.log(H.gray("  Git changes were pushed successfully.")),process.exit(1)}await A1(F),$.succeed(`Copied ${q.filesCopied} file(s) to S3`)}else console.log(H.gray("  No S3 remote configured; skipping data push."))}if(D.pr){let Q=await M9(F);if(!Q)console.log(H.red("  Could not determine current branch")),console.log(H.gray("  Ensure you are inside a valid git repository.")),process.exit(1);if(Q==="main"||Q==="master")console.log(H.yellow("  Skipping PR: already on main branch"));else{$=N("Creating pull request...").start();let B=["gh","pr","create"];if(D.title)B.push("--title",D.title);else B.push("--title",`Update from branch ${Q}`);if(D.body)B.push("--body",D.body);else B.push("--body","");try{let Y=QD({cmd:B,cwd:F,env:process.env,stdout:"pipe",stderr:"pipe"}),X=await new Response(Y.stdout).text(),G=await new Response(Y.stderr).text();if(await Y.exited!==0)$.fail("Failed to create pull request"),console.log(H.red(`  ${G.trim()||X.trim()}`)),process.exit(1);let q=X.trim();$.succeed("Pull request created"),console.log(`  ${H.cyan(q)}`)}catch(Y){$.fail("Failed to create pull request");let X=Y instanceof Error?Y.message:String(Y);if(X.includes("ENOENT")||X.includes("not found"))console.log(H.red("  'gh' CLI is not installed or not in PATH")),console.log(H.gray("  Install it: https://cli.github.com/"));else console.log(H.red(`  ${X}`));process.exit(1)}}}});DD.command("drop").description("Free local copies of annexed files (keeps remote copies)").argument("[files...]","Specific files to drop (default: all)").addHelpText("after",`
+  $ nemar dataset push --pr -t "Add new recordings"`).action(async(D)=>{let F=process.cwd();if(!await p8(F))console.log(H.red("Error: Not inside a git-annex dataset directory")),process.exit(1);let $=N("Pushing to GitHub...").start(),J=await Z8(F);if(!J.success)$.fail("Git push failed"),console.log(H.red(`  ${J.error}`)),process.exit(1);if(J.warning)$.warn("Git pushed with warning"),console.log(H.yellow(`  ${J.warning}`));else $.succeed("Pushed to GitHub");if(D.s3!==!1){let Q=await pJ(F);if(Q.length>0){let B=Q[0];if(Q.length>1)console.log(H.dim(`  Multiple S3 remotes: ${Q.join(", ")}. Using: ${B}`));let Y=Number.parseInt(D.jobs,10);if(Number.isNaN(Y)||Y<1)console.log(H.red("Error: --jobs must be a positive integer")),process.exit(1);let X=await UF(F),G=null;if(X&&v0()){$=N("Requesting upload credentials...").start();try{G=await R4(X),$.succeed("Upload credentials received")}catch(K){$.warn(`Could not get upload credentials: ${p0(K)}. Trying environment credentials.`)}}$=N(`Copying data to S3 (${B})...`).start();let W=G?nD(G.credentials):void 0,q=await T4(F,B,Y,W);if(!q.success){if($.fail("S3 push failed"),console.log(H.red(`  ${q.error}`)),!G)console.log(H.dim("  Ensure AWS_ACCESS_KEY_ID and AWS_SECRET_ACCESS_KEY are set,")),console.log(H.dim("  or log in with 'nemar auth login' for automatic credentials."));console.log(H.dim("  Git changes were pushed successfully.")),process.exit(1)}await A1(F),$.succeed(`Copied ${q.filesCopied} file(s) to S3`)}else console.log(H.dim("  No S3 remote configured; skipping data push."))}if(D.pr){let Q=await M9(F);if(!Q)console.log(H.red("  Could not determine current branch")),console.log(H.dim("  Ensure you are inside a valid git repository.")),process.exit(1);if(Q==="main"||Q==="master")console.log(H.yellow("  Skipping PR: already on main branch"));else{$=N("Creating pull request...").start();let B=["gh","pr","create"];if(D.title)B.push("--title",D.title);else B.push("--title",`Update from branch ${Q}`);if(D.body)B.push("--body",D.body);else B.push("--body","");try{let Y=QD({cmd:B,cwd:F,env:process.env,stdout:"pipe",stderr:"pipe"}),X=await new Response(Y.stdout).text(),G=await new Response(Y.stderr).text();if(await Y.exited!==0)$.fail("Failed to create pull request"),console.log(H.red(`  ${G.trim()||X.trim()}`)),process.exit(1);let q=X.trim();$.succeed("Pull request created"),console.log(`  ${H.cyan(q)}`)}catch(Y){$.fail("Failed to create pull request");let X=Y instanceof Error?Y.message:String(Y);if(X.includes("ENOENT")||X.includes("not found"))console.log(H.red("  'gh' CLI is not installed or not in PATH")),console.log(H.dim("  Install it: https://cli.github.com/"));else console.log(H.red(`  ${X}`));process.exit(1)}}}});DD.command("drop").description("Free local copies of annexed files (keeps remote copies)").argument("[files...]","Specific files to drop (default: all)").addHelpText("after",`
 Description:
   Remove local copies of annexed data files. Git-annex verifies that
   remote copies exist before dropping. Use 'nemar dataset get' to
@@ -791,7 +789,7 @@ Description:
 Examples:
   $ nemar dataset drop                   # Drop all local data
   $ nemar dataset drop sub-01/eeg/       # Drop specific directory
-  $ nemar dataset drop *.edf             # Drop EDF files`).action(async(D)=>{let F=process.cwd();if(!await p8(F))console.log(H.red("Error: Not inside a git-annex dataset directory")),process.exit(1);let $=D.length>0?D:void 0,J=$?`Dropping ${$.length} path(s)...`:"Dropping all local data...",Q=N(J).start(),B=await Gf(F,$);if(!B.success&&B.dropped===0)Q.fail("Drop failed"),console.log(H.red(`  ${B.error}`)),process.exit(1);if(B.kept.length>0){Q.warn(`Dropped ${B.dropped} file(s), ${B.kept.length} kept (no remote copy)`);for(let Y of B.kept.slice(0,5))console.log(H.yellow(`  kept: ${Y}`));if(B.kept.length>5)console.log(H.yellow(`  ... and ${B.kept.length-5} more`));if(B.error)console.log(H.gray(`  ${B.error}`));process.exit(1)}else Q.succeed(`Dropped ${B.dropped} file(s)`)});DD.command("ci").description("Check BIDS validation CI status for the current dataset").argument("[dataset-id]","Dataset ID (auto-detected from git remote if omitted)").addHelpText("after",`
+  $ nemar dataset drop *.edf             # Drop EDF files`).action(async(D)=>{let F=process.cwd();if(!await p8(F))console.log(H.red("Error: Not inside a git-annex dataset directory")),process.exit(1);let $=D.length>0?D:void 0,J=$?`Dropping ${$.length} path(s)...`:"Dropping all local data...",Q=N(J).start(),B=await Gf(F,$);if(!B.success&&B.dropped===0)Q.fail("Drop failed"),console.log(H.red(`  ${B.error}`)),process.exit(1);if(B.kept.length>0){Q.warn(`Dropped ${B.dropped} file(s), ${B.kept.length} kept (no remote copy)`);for(let Y of B.kept.slice(0,5))console.log(H.yellow(`  kept: ${Y}`));if(B.kept.length>5)console.log(H.yellow(`  ... and ${B.kept.length-5} more`));if(B.error)console.log(H.dim(`  ${B.error}`));process.exit(1)}else Q.succeed(`Dropped ${B.dropped} file(s)`)});DD.command("ci").description("Check BIDS validation CI status for the current dataset").argument("[dataset-id]","Dataset ID (auto-detected from git remote if omitted)").addHelpText("after",`
 Description:
   Show the status of the BIDS validation CI workflow for a dataset.
   When run inside a cloned dataset, the dataset ID is auto-detected
@@ -799,7 +797,7 @@ Description:
 Examples:
   $ nemar dataset ci              # Auto-detect from CWD
-  $ nemar dataset ci nm000104     # Explicit dataset ID`).action(async(D)=>{if(!v0())console.log(H.red("Error: Not authenticated")),console.log("Run 'nemar auth login' first"),process.exit(1);let F=D;if(!F){let J=process.cwd();if(await p8(J))F=await UF(J);if(!F)console.log(H.red("Error: Could not detect dataset ID from current directory")),console.log(H.gray("Provide dataset ID explicitly: nemar dataset ci <id>")),process.exit(1)}let $=N(`Checking CI status for ${F}...`).start();try{let J=await w_(F);$.stop(),console.log(H.bold(`CI Status: ${F}`)),console.log();let{bids_validation:Q}=J;if(!Q.present)console.log(`  BIDS Validation: ${H.gray("not configured")}`),console.log(H.gray(`  Ask an admin to run: nemar admin ci add ${F}`));else{let B=Q.status==="success"?H.green:Q.status==="failure"?H.red:H.yellow;if(console.log(`  BIDS Validation: ${B(Q.status)}`),Q.url)console.log(`  Latest run: ${H.cyan(Q.url)}`)}console.log()}catch(J){if(J instanceof i)$.fail(J.message);else{$.fail("Failed to check CI status");let Q=J instanceof Error?J.message:String(J);console.log(H.gray(`  ${Q}`))}process.exit(1)}});DD.command("manifest").description("View version manifests for a dataset").argument("[version]","Version to view (lists available if omitted)").option("-d, --dataset <id>","Dataset ID (auto-detected from git remote if omitted)").option("--json","Output raw JSON").addHelpText("after",`
+  $ nemar dataset ci nm000104     # Explicit dataset ID`).action(async(D)=>{if(!v0())console.log(H.red("Error: Not authenticated")),console.log("Run 'nemar auth login' first"),process.exit(1);let F=D;if(!F){let J=process.cwd();if(await p8(J))F=await UF(J);if(!F)console.log(H.red("Error: Could not detect dataset ID from current directory")),console.log(H.dim("Provide dataset ID explicitly: nemar dataset ci <id>")),process.exit(1)}let $=N(`Checking CI status for ${F}...`).start();try{let J=await w_(F);$.stop(),console.log(H.bold(`CI Status: ${F}`)),console.log();let{bids_validation:Q}=J;if(!Q.present)console.log(`  BIDS Validation: ${H.dim("not configured")}`),console.log(H.dim(`  Ask an admin to run: nemar admin ci add ${F}`));else{let B=Q.status==="success"?H.green:Q.status==="failure"?H.red:H.yellow;if(console.log(`  BIDS Validation: ${B(Q.status)}`),Q.url)console.log(`  Latest run: ${H.cyan(Q.url)}`)}console.log()}catch(J){if(J instanceof i)$.fail(J.message);else{$.fail("Failed to check CI status");let Q=J instanceof Error?J.message:String(J);console.log(H.dim(`  ${Q}`))}process.exit(1)}});DD.command("manifest").description("View version manifests for a dataset").argument("[version]","Version to view (lists available if omitted)").option("-d, --dataset <id>","Dataset ID (auto-detected from git remote if omitted)").option("--json","Output raw JSON").addHelpText("after",`
 Description:
   View version manifests that map file paths to S3 annex keys.
   Manifests are generated when a version DOI is published.
@@ -810,7 +808,7 @@ Examples:
   $ nemar dataset manifest                    # List available versions
   $ nemar dataset manifest v1.0.0             # View specific version
   $ nemar dataset manifest v1.0.0 --json      # Raw JSON output
-  $ nemar dataset manifest -d nm000104        # Explicit dataset ID`).action(async(D,F)=>{if(!v0())console.log(H.red("Error: Not authenticated")),console.log("Run 'nemar auth login' first"),process.exit(1);let $=F.dataset;if(!$){let Q=process.cwd();if(await p8(Q))$=await UF(Q);if(!$)console.log(H.red("Error: Could not detect dataset ID")),console.log(H.gray("Provide dataset ID: nemar dataset manifest -d <id>")),process.exit(1)}let J=N("Fetching manifest info...").start();try{if(!D){let Q=await T_($);if(J.stop(),console.log(H.bold(`Manifests: ${$}`)),console.log(),Q.versions.length===0)console.log(H.gray("  No manifests available yet.")),console.log(H.gray("  Manifests are generated when a version DOI is published."));else for(let B of Q.versions)console.log(`  ${H.cyan(B)}`);console.log()}else{let Q=await j_($,D);if(J.stop(),F.json)console.log(JSON.stringify(Q,null,2));else{if(console.log(H.bold(`Manifest: ${$} ${Q.version}`)),Q.doi)console.log(`  DOI: ${H.cyan(Q.doi)}`);if(Q.concept_doi)console.log(`  Concept DOI: ${H.gray(Q.concept_doi)}`);console.log(`  Created: ${Q.created}`),console.log();let B=Object.entries(Q.files),Y=B.filter(([,G])=>!G.key.startsWith("git:")),X=B.filter(([,G])=>G.key.startsWith("git:"));if(Y.length>0){console.log(H.bold(`  Annexed files (${Y.length}):`));for(let[G,W]of Y){let q=Og(W.size);console.log(`    ${G} ${H.gray(`(${q})`)}`)}}if(X.length>0){console.log(),console.log(H.bold(`  Metadata files (${X.length}):`));for(let[G,W]of X){let q=Og(W.size);console.log(`    ${G} ${H.gray(`(${q})`)}`)}}console.log()}}}catch(Q){if(Q instanceof i)J.fail(Q.message);else{J.fail("Failed to fetch manifest");let B=Q instanceof Error?Q.message:String(Q);console.log(H.gray(`  ${B}`))}process.exit(1)}});function Og(D){if(D===0)return"0 B";let F=["B","KB","MB","GB","TB"],$=Math.floor(Math.log(D)/Math.log(1024));return`${(D/1024**$).toFixed($>0?1:0)} ${F[$]}`}N1();v3();O4();KF();j4();import{mkdirSync as xE0,rmSync as _E0,writeFileSync as I9}from"fs";import{tmpdir as fE0}from"os";import{join as u6}from"path";function gE0(D){let F=u6(D,"sub-01"),$=u6(F,"eeg");return{root:D,datasetDescription:u6(D,"dataset_description.json"),participants:u6(D,"participants.tsv"),readme:u6(D,"README"),subjectDir:F,eegDir:$,edfFile:u6($,"sub-01_task-rest_eeg.edf"),sidecarJson:u6($,"sub-01_task-rest_eeg.json")}}function jg(D){let F=D||u6(fE0(),`nemar-sandbox-${Date.now()}`),$=gE0(F);xE0($.eegDir,{recursive:!0});let J={Name:"NEMAR Sandbox Training Dataset",BIDSVersion:"1.9.0",DatasetType:"raw",License:"CC0",Authors:["NEMAR CLI Training"],HowToAcknowledge:"This is a sandbox dataset for testing the NEMAR upload workflow.",DatasetDOI:"n/a"};I9($.datasetDescription,JSON.stringify(J,null,2));let Q=`participant_id	age	sex
+  $ nemar dataset manifest -d nm000104        # Explicit dataset ID`).action(async(D,F)=>{if(!v0())console.log(H.red("Error: Not authenticated")),console.log("Run 'nemar auth login' first"),process.exit(1);let $=F.dataset;if(!$){let Q=process.cwd();if(await p8(Q))$=await UF(Q);if(!$)console.log(H.red("Error: Could not detect dataset ID")),console.log(H.dim("Provide dataset ID: nemar dataset manifest -d <id>")),process.exit(1)}let J=N("Fetching manifest info...").start();try{if(!D){let Q=await T_($);if(J.stop(),console.log(H.bold(`Manifests: ${$}`)),console.log(),Q.versions.length===0)console.log(H.dim("  No manifests available yet.")),console.log(H.dim("  Manifests are generated when a version DOI is published."));else for(let B of Q.versions)console.log(`  ${H.cyan(B)}`);console.log()}else{let Q=await j_($,D);if(J.stop(),F.json)console.log(JSON.stringify(Q,null,2));else{if(console.log(H.bold(`Manifest: ${$} ${Q.version}`)),Q.doi)console.log(`  DOI: ${H.cyan(Q.doi)}`);if(Q.concept_doi)console.log(`  Concept DOI: ${H.dim(Q.concept_doi)}`);console.log(`  Created: ${Q.created}`),console.log();let B=Object.entries(Q.files),Y=B.filter(([,G])=>!G.key.startsWith("git:")),X=B.filter(([,G])=>G.key.startsWith("git:"));if(Y.length>0){console.log(H.bold(`  Annexed files (${Y.length}):`));for(let[G,W]of Y){let q=Og(W.size);console.log(`    ${G} ${H.dim(`(${q})`)}`)}}if(X.length>0){console.log(),console.log(H.bold(`  Metadata files (${X.length}):`));for(let[G,W]of X){let q=Og(W.size);console.log(`    ${G} ${H.dim(`(${q})`)}`)}}console.log()}}}catch(Q){if(Q instanceof i)J.fail(Q.message);else{J.fail("Failed to fetch manifest");let B=Q instanceof Error?Q.message:String(Q);console.log(H.dim(`  ${B}`))}process.exit(1)}});function Og(D){if(D===0)return"0 B";let F=["B","KB","MB","GB","TB"],$=Math.floor(Math.log(D)/Math.log(1024));return`${(D/1024**$).toFixed($>0?1:0)} ${F[$]}`}N1();v3();O4();KF();j4();import{mkdirSync as xE0,rmSync as _E0,writeFileSync as I9}from"fs";import{tmpdir as fE0}from"os";import{join as u6}from"path";function gE0(D){let F=u6(D,"sub-01"),$=u6(F,"eeg");return{root:D,datasetDescription:u6(D,"dataset_description.json"),participants:u6(D,"participants.tsv"),readme:u6(D,"README"),subjectDir:F,eegDir:$,edfFile:u6($,"sub-01_task-rest_eeg.edf"),sidecarJson:u6($,"sub-01_task-rest_eeg.json")}}function jg(D){let F=D||u6(fE0(),`nemar-sandbox-${Date.now()}`),$=gE0(F);xE0($.eegDir,{recursive:!0});let J={Name:"NEMAR Sandbox Training Dataset",BIDSVersion:"1.9.0",DatasetType:"raw",License:"CC0",Authors:["NEMAR CLI Training"],HowToAcknowledge:"This is a sandbox dataset for testing the NEMAR upload workflow.",DatasetDOI:"n/a"};I9($.datasetDescription,JSON.stringify(J,null,2));let Q=`participant_id	age	sex
 sub-01	25	M
 `;I9($.participants,Q);let B=`# NEMAR Sandbox Training Dataset
@@ -845,7 +843,7 @@ Examples:
   $ nemar sandbox           # Run sandbox training
   $ nemar sandbox status    # Check if training is completed
   $ nemar sandbox reset     # Reset for re-training
-`).action(bE0);async function bE0(){if(console.log(),console.log(H.bold("NEMAR Sandbox Training")),console.log(H.gray("Verify your setup and learn the upload workflow")),console.log(),!v0()){console.log(H.red("Not authenticated")),console.log(H.gray("Run 'nemar auth login' first"));return}let D=YD();if(D.sandboxCompleted){console.log(H.green("Sandbox training already completed!")),console.log(H.gray(`Dataset ID: ${D.sandboxDatasetId}`)),console.log(),console.log("You can upload real datasets with:"),console.log(H.cyan("  nemar dataset upload ./your-dataset")),console.log(),console.log(H.gray("To re-run training, use: nemar sandbox reset"));return}console.log(H.bold("Step 1/6: Checking prerequisites..."));let F=N("Checking git-annex and SSH...").start(),$=await uJ();if(!$.allPassed){F.fail("Prerequisites check failed"),console.log(),console.log(H.red("Missing requirements:"));for(let I of $.errors)console.log(H.yellow(`  - ${I}`));if(!$.githubSSH.accessible)console.log(H.gray("    Run 'nemar auth setup-ssh' to configure SSH"));return}F.succeed("All prerequisites met");let J=N("Verifying GitHub CLI authentication...").start(),Q=await mJ(D.githubUsername);if(!Q.authenticated){J.fail("GitHub CLI not authenticated"),console.log(H.red(`  ${Q.error}`)),console.log(),console.log("GitHub CLI is required for sandbox training. Install and authenticate:"),console.log(H.cyan("  brew install gh       # or visit https://cli.github.com/")),console.log(H.cyan("  gh auth login"));return}if(D.githubUsername&&!Q.matches)J.warn("GitHub CLI user mismatch"),console.log(H.yellow(`  ${Q.error}`)),console.log(),console.log("Your gh CLI is authenticated as a different GitHub account than your NEMAR account."),console.log("This may cause issues with repository access. To fix:"),console.log(H.cyan(`  gh auth login    # Login as ${D.githubUsername}`)),console.log(),console.log(H.yellow("WARNING: If upload fails with permission errors, this mismatch is the likely cause.")),console.log();else J.succeed(`GitHub CLI authenticated as ${Q.username}`);console.log(),console.log(H.bold("Step 2/6: Generating test dataset..."));let B=N("Creating minimal BIDS structure...").start(),Y;try{let I=jg();Y=I.root;let T=Pg(I);B.succeed(`Test dataset created (${V8(T)})`),console.log(H.gray(`  Location: ${Y}`))}catch(I){B.fail("Failed to generate test dataset"),console.log(H.red(`  ${I instanceof Error?I.message:"Unknown error"}`));return}console.log(),console.log(H.bold("Step 3/6: Registering sandbox dataset..."));let X=N("Creating dataset on NEMAR...").start(),G,W,q,K,Z,z;try{let I=await _J({name:"Sandbox Training Dataset",description:"Placeholder dataset for sandbox training",files:[{path:"sub-01/eeg/sub-01_task-rest_eeg.edf",size:512000,type:"data"},{path:"dataset_description.json",size:200,type:"metadata"},{path:"participants.tsv",size:50,type:"metadata"},{path:"README",size:500,type:"metadata"},{path:"sub-01/eeg/sub-01_task-rest_eeg.json",size:300,type:"metadata"}],sandbox:!0});G=I.dataset.dataset_id,W=I.dataset.ssh_url,q=I.dataset.github_url,K=I.s3_config,Z=I.dataset.s3_prefix,z=I.upload_urls||{},X.succeed(`Sandbox dataset created: ${H.cyan(G)}`),console.log(H.gray(`  GitHub: ${q}`)),await new Promise((T)=>setTimeout(T,1e4))}catch(I){if(X.fail("Failed to create sandbox dataset"),I instanceof i)console.log(H.red(`  ${I.message}`));else console.log(H.red(`  ${I instanceof Error?I.message:"Unknown error"}`));d1(Y);return}let U=N("Accepting GitHub repository invitation...").start(),A=q?.match(/github\.com\/([a-zA-Z0-9_.-]+\/[a-zA-Z0-9_.-]+)/),M=A?A[1].replace(/\.git$/,""):null;if(!M){U.fail("Invalid GitHub repository URL from backend"),console.log(H.red(`  Received: ${q||"(empty)"}`)),console.log(H.red("  Expected format: https://github.com/owner/repo")),console.log(),console.log("This may indicate a backend issue. Please contact support."),d1(Y);return}let L=await lJ(M);if(L.accepted)if(L.alreadyCollaborator)U.succeed("Already a collaborator on this repository");else U.succeed("GitHub invitation accepted");else U.warn("Could not auto-accept invitation"),console.log(H.yellow(`  ${L.error}`)),console.log(),console.log("You may need to accept the invitation manually:"),console.log(H.cyan(`  https://github.com/${M}/invitations`)),console.log();console.log(),console.log(H.bold("Step 4/6: Initializing repository..."));let C=N("Setting up git-annex...").start(),O=D.username&&D.email?{name:D.username,email:D.email}:void 0;try{await zF(Y,{author:O}),await VF(Y),await f6(Y,W),C.succeed("Repository initialized")}catch(I){C.fail("Failed to initialize repository"),console.log(H.red(`  ${I instanceof Error?I.message:"Unknown error"}`)),d1(Y);return}if(console.log(),console.log(H.bold("Step 5/6: Uploading to S3...")),Object.keys(z).length===0)console.log(H.yellow("  No data files to upload (metadata only)"));else{let I=N("Uploading test data...").start();try{let f=0,n=Object.keys(z).length,s=await Yf(Y,z,{jobs:4,onProgress:(h)=>{if(h.status==="completed"||h.status==="failed")f++,I.text=`Uploading... ${f}/${n} files`}});if(s.failed.length>0){I.fail(`Upload failed for ${s.failed.length} file(s)`);for(let h of s.failed)console.log(H.red(`    Failed: ${h}`));if(s.error)console.log(H.red(`    Error: ${s.error}`));console.log(),console.log(H.yellow("Sandbox training aborted due to upload failures.")),console.log(H.gray("Please check your network connection and try again.")),d1(Y);return}I.succeed(`Uploaded ${s.uploaded} file(s)`)}catch(f){I.fail("Upload failed"),console.log(H.red(`  ${f instanceof Error?f.message:"Unknown error"}`)),d1(Y);return}let T=N("Registering file URLs...").start();try{let f={};for(let s of Object.keys(z))f[s]=`${K.public_url}/${Z}/objects/${s}`;let n=await Xf(Y,f);if(!n.success){T.fail(`URL registration failed for ${n.failed.length} file(s)`);for(let s of n.failed)console.log(H.red(`    Failed: ${s}`));console.log(),console.log(H.yellow("Sandbox training aborted due to URL registration failures.")),console.log(H.gray("This may indicate a git-annex configuration issue.")),d1(Y);return}T.succeed(`Registered ${n.registered} file URLs`)}catch(f){T.fail("Failed to register URLs"),console.log(H.red(`  ${f instanceof Error?f.message:"Unknown error"}`)),d1(Y);return}}console.log(),console.log(H.bold("Step 6/6: Pushing to GitHub..."));let y=N("Saving and pushing...").start();try{await g6(Y,"Initial sandbox training upload",O),await Z8(Y),y.succeed("Pushed to GitHub")}catch(I){y.fail("Failed to push to GitHub"),console.log(H.red(`  ${I instanceof Error?I.message:"Unknown error"}`)),d1(Y);return}let w=N("Finalizing...").start();try{await fJ(G),await __(G),l8("sandboxCompleted",!0),l8("sandboxDatasetId",G),w.succeed("Sandbox training complete!")}catch(I){w.fail("Failed to finalize"),console.log(H.red(`  ${I instanceof Error?I.message:"Unknown error"}`)),d1(Y);return}d1(Y),console.log(),console.log(H.green.bold("Congratulations! Sandbox training completed successfully.")),console.log(),console.log("Your setup is verified and you're ready to upload real datasets:"),console.log(H.cyan("  nemar dataset upload ./your-dataset")),console.log(),console.log(H.gray(`Sandbox dataset: ${G}`))}FQ.command("status").description("Check sandbox training completion status").option("--refresh","Fetch latest status from server").action(async(D)=>{if(!v0()){console.log(H.red("Not authenticated")),console.log(H.gray("Run 'nemar auth login' first"));return}if(D.refresh){let F=N("Checking status...").start();try{let $=await g_();if(l8("sandboxCompleted",$.sandbox_completed),$.sandbox_dataset_id)l8("sandboxDatasetId",$.sandbox_dataset_id);if(F.stop(),$.sandbox_completed){if(console.log(H.green("Sandbox training: Completed")),console.log(H.gray(`  Dataset ID: ${$.sandbox_dataset_id}`)),$.sandbox_completed_at)console.log(H.gray(`  Completed: ${$.sandbox_completed_at}`))}else console.log(H.yellow("Sandbox training: Not completed")),console.log(),console.log("Run sandbox training with:"),console.log(H.cyan("  nemar sandbox"))}catch($){if(F.fail("Failed to check status"),$ instanceof i)console.log(H.red(`  ${$.message}`))}}else{let F=YD();if(F.sandboxCompleted)console.log(H.green("Sandbox training: Completed")),console.log(H.gray(`  Dataset ID: ${F.sandboxDatasetId}`));else console.log(H.yellow("Sandbox training: Not completed")),console.log(),console.log("Run sandbox training with:"),console.log(H.cyan("  nemar sandbox"))}});FQ.command("reset").description("Reset sandbox training status for re-training").option(I0,S0).option(a0,g0).action(async(D)=>{if(!v0()){console.log(H.red("Not authenticated")),console.log(H.gray("Run 'nemar auth login' first"));return}if(!YD().sandboxCompleted){console.log(H.yellow("Sandbox training not yet completed")),console.log(H.gray("Nothing to reset"));return}let $=await y0("Reset sandbox training status? You will need to complete training again.",D);if($!=="confirmed"){console.log(H.gray($==="declined"?"Skipped":"Cancelled"));return}let J=N("Resetting sandbox status...").start();try{await f_(),sG("sandboxCompleted"),sG("sandboxDatasetId"),J.succeed("Sandbox status reset"),console.log(),console.log("Run sandbox training again with:"),console.log(H.cyan("  nemar sandbox"))}catch(Q){if(J.fail("Failed to reset"),Q instanceof i)console.log(H.red(`  ${Q.message}`));else console.log(H.red(`  ${Q instanceof Error?Q.message:"Unknown error"}`))}});rG();var F1=new FD;F1.name("nemar").description(`CLI for NEMAR (Neuroelectromagnetic Data Archive and Tools Resource)
+`).action(bE0);async function bE0(){if(console.log(),console.log(H.bold("NEMAR Sandbox Training")),console.log(H.dim("Verify your setup and learn the upload workflow")),console.log(),!v0()){console.log(H.red("Not authenticated")),console.log(H.dim("Run 'nemar auth login' first"));return}let D=YD();if(D.sandboxCompleted){console.log(H.green("Sandbox training already completed!")),console.log(H.dim(`Dataset ID: ${D.sandboxDatasetId}`)),console.log(),console.log("You can upload real datasets with:"),console.log(H.cyan("  nemar dataset upload ./your-dataset")),console.log(),console.log(H.dim("To re-run training, use: nemar sandbox reset"));return}console.log(H.bold("Step 1/6: Checking prerequisites..."));let F=N("Checking prerequisites...").start(),$=await uJ();if(!$.allPassed){F.fail("Prerequisites check failed"),console.log(),console.log(H.red("Missing requirements:"));for(let I of $.errors)console.log(H.yellow(`  - ${I}`));if($.errors.some((I)=>I.includes("GitHub")))console.log(H.dim("    Run 'gh auth login' to authenticate with GitHub"));return}F.succeed("All prerequisites met");let J=N("Verifying GitHub CLI authentication...").start(),Q=await mJ(D.githubUsername);if(!Q.authenticated){J.fail("GitHub CLI not authenticated"),console.log(H.red(`  ${Q.error}`)),console.log(),console.log("GitHub CLI is required for sandbox training. Install and authenticate:"),console.log(H.cyan("  brew install gh       # or visit https://cli.github.com/")),console.log(H.cyan("  gh auth login"));return}if(D.githubUsername&&!Q.matches)J.warn("GitHub CLI user mismatch"),console.log(H.yellow(`  ${Q.error}`)),console.log(),console.log("Your gh CLI is authenticated as a different GitHub account than your NEMAR account."),console.log("This may cause issues with repository access. To fix:"),console.log(H.cyan(`  gh auth login    # Login as ${D.githubUsername}`)),console.log(),console.log(H.yellow("WARNING: If upload fails with permission errors, this mismatch is the likely cause.")),console.log();else J.succeed(`GitHub CLI authenticated as ${Q.username}`);console.log(),console.log(H.bold("Step 2/6: Generating test dataset..."));let B=N("Creating minimal BIDS structure...").start(),Y;try{let I=jg();Y=I.root;let T=Pg(I);B.succeed(`Test dataset created (${V8(T)})`),console.log(H.dim(`  Location: ${Y}`))}catch(I){B.fail("Failed to generate test dataset"),console.log(H.red(`  ${I instanceof Error?I.message:"Unknown error"}`));return}console.log(),console.log(H.bold("Step 3/6: Registering sandbox dataset..."));let X=N("Creating dataset on NEMAR...").start(),G,W,q,K,Z,z;try{let I=await _J({name:"Sandbox Training Dataset",description:"Placeholder dataset for sandbox training",files:[{path:"sub-01/eeg/sub-01_task-rest_eeg.edf",size:512000,type:"data"},{path:"dataset_description.json",size:200,type:"metadata"},{path:"participants.tsv",size:50,type:"metadata"},{path:"README",size:500,type:"metadata"},{path:"sub-01/eeg/sub-01_task-rest_eeg.json",size:300,type:"metadata"}],sandbox:!0});G=I.dataset.dataset_id,W=I.dataset.ssh_url,q=I.dataset.github_url,K=I.s3_config,Z=I.dataset.s3_prefix,z=I.upload_urls||{},X.succeed(`Sandbox dataset created: ${H.cyan(G)}`),console.log(H.dim(`  GitHub: ${q}`)),await new Promise((T)=>setTimeout(T,1e4))}catch(I){if(X.fail("Failed to create sandbox dataset"),I instanceof i)console.log(H.red(`  ${I.message}`));else console.log(H.red(`  ${I instanceof Error?I.message:"Unknown error"}`));d1(Y);return}let U=N("Accepting GitHub repository invitation...").start(),A=q?.match(/github\.com\/([a-zA-Z0-9_.-]+\/[a-zA-Z0-9_.-]+)/),M=A?A[1].replace(/\.git$/,""):null;if(!M){U.fail("Invalid GitHub repository URL from backend"),console.log(H.red(`  Received: ${q||"(empty)"}`)),console.log(H.red("  Expected format: https://github.com/owner/repo")),console.log(),console.log("This may indicate a backend issue. Please contact support."),d1(Y);return}let L=await lJ(M);if(L.accepted)if(L.alreadyCollaborator)U.succeed("Already a collaborator on this repository");else U.succeed("GitHub invitation accepted");else U.warn("Could not auto-accept invitation"),console.log(H.yellow(`  ${L.error}`)),console.log(),console.log("You may need to accept the invitation manually:"),console.log(H.cyan(`  https://github.com/${M}/invitations`)),console.log();console.log(),console.log(H.bold("Step 4/6: Initializing repository..."));let C=N("Setting up git-annex...").start(),O=D.username&&D.email?{name:D.username,email:D.email}:void 0;try{await zF(Y,{author:O}),await VF(Y),await f6(Y,W),C.succeed("Repository initialized")}catch(I){C.fail("Failed to initialize repository"),console.log(H.red(`  ${I instanceof Error?I.message:"Unknown error"}`)),d1(Y);return}if(console.log(),console.log(H.bold("Step 5/6: Uploading to S3...")),Object.keys(z).length===0)console.log(H.yellow("  No data files to upload (metadata only)"));else{let I=N("Uploading test data...").start();try{let f=0,n=Object.keys(z).length,s=await Yf(Y,z,{jobs:4,onProgress:(h)=>{if(h.status==="completed"||h.status==="failed")f++,I.text=`Uploading... ${f}/${n} files`}});if(s.failed.length>0){I.fail(`Upload failed for ${s.failed.length} file(s)`);for(let h of s.failed)console.log(H.red(`    Failed: ${h}`));if(s.error)console.log(H.red(`    Error: ${s.error}`));console.log(),console.log(H.yellow("Sandbox training aborted due to upload failures.")),console.log(H.dim("Please check your network connection and try again.")),d1(Y);return}I.succeed(`Uploaded ${s.uploaded} file(s)`)}catch(f){I.fail("Upload failed"),console.log(H.red(`  ${f instanceof Error?f.message:"Unknown error"}`)),d1(Y);return}let T=N("Registering file URLs...").start();try{let f={};for(let s of Object.keys(z))f[s]=`${K.public_url}/${Z}/objects/${s}`;let n=await Xf(Y,f);if(!n.success){T.fail(`URL registration failed for ${n.failed.length} file(s)`);for(let s of n.failed)console.log(H.red(`    Failed: ${s}`));console.log(),console.log(H.yellow("Sandbox training aborted due to URL registration failures.")),console.log(H.dim("This may indicate a git-annex configuration issue.")),d1(Y);return}T.succeed(`Registered ${n.registered} file URLs`)}catch(f){T.fail("Failed to register URLs"),console.log(H.red(`  ${f instanceof Error?f.message:"Unknown error"}`)),d1(Y);return}}console.log(),console.log(H.bold("Step 6/6: Pushing to GitHub..."));let y=N("Saving and pushing...").start();try{await g6(Y,"Initial sandbox training upload",O),await Z8(Y),y.succeed("Pushed to GitHub")}catch(I){y.fail("Failed to push to GitHub"),console.log(H.red(`  ${I instanceof Error?I.message:"Unknown error"}`)),d1(Y);return}let w=N("Finalizing...").start();try{await fJ(G),await __(G),l8("sandboxCompleted",!0),l8("sandboxDatasetId",G),w.succeed("Sandbox training complete!")}catch(I){w.fail("Failed to finalize"),console.log(H.red(`  ${I instanceof Error?I.message:"Unknown error"}`)),d1(Y);return}d1(Y),console.log(),console.log(H.green.bold("Congratulations! Sandbox training completed successfully.")),console.log(),console.log("Your setup is verified and you're ready to upload real datasets:"),console.log(H.cyan("  nemar dataset upload ./your-dataset")),console.log(),console.log(H.dim(`Sandbox dataset: ${G}`))}FQ.command("status").description("Check sandbox training completion status").option("--refresh","Fetch latest status from server").action(async(D)=>{if(!v0()){console.log(H.red("Not authenticated")),console.log(H.dim("Run 'nemar auth login' first"));return}if(D.refresh){let F=N("Checking status...").start();try{let $=await g_();if(l8("sandboxCompleted",$.sandbox_completed),$.sandbox_dataset_id)l8("sandboxDatasetId",$.sandbox_dataset_id);if(F.stop(),$.sandbox_completed){if(console.log(H.green("Sandbox training: Completed")),console.log(H.dim(`  Dataset ID: ${$.sandbox_dataset_id}`)),$.sandbox_completed_at)console.log(H.dim(`  Completed: ${$.sandbox_completed_at}`))}else console.log(H.yellow("Sandbox training: Not completed")),console.log(),console.log("Run sandbox training with:"),console.log(H.cyan("  nemar sandbox"))}catch($){if(F.fail("Failed to check status"),$ instanceof i)console.log(H.red(`  ${$.message}`))}}else{let F=YD();if(F.sandboxCompleted)console.log(H.green("Sandbox training: Completed")),console.log(H.dim(`  Dataset ID: ${F.sandboxDatasetId}`));else console.log(H.yellow("Sandbox training: Not completed")),console.log(),console.log("Run sandbox training with:"),console.log(H.cyan("  nemar sandbox"))}});FQ.command("reset").description("Reset sandbox training status for re-training").option(I0,S0).option(a0,g0).action(async(D)=>{if(!v0()){console.log(H.red("Not authenticated")),console.log(H.dim("Run 'nemar auth login' first"));return}if(!YD().sandboxCompleted){console.log(H.yellow("Sandbox training not yet completed")),console.log(H.dim("Nothing to reset"));return}let $=await y0("Reset sandbox training status? You will need to complete training again.",D);if($!=="confirmed"){console.log(H.dim($==="declined"?"Skipped":"Cancelled"));return}let J=N("Resetting sandbox status...").start();try{await f_(),sG("sandboxCompleted"),sG("sandboxDatasetId"),J.succeed("Sandbox status reset"),console.log(),console.log("Run sandbox training again with:"),console.log(H.cyan("  nemar sandbox"))}catch(Q){if(J.fail("Failed to reset"),Q instanceof i)console.log(H.red(`  ${Q.message}`));else console.log(H.red(`  ${Q instanceof Error?Q.message:"Unknown error"}`))}});rG();var F1=new FD;F1.name("nemar").description(`CLI for NEMAR (Neuroelectromagnetic Data Archive and Tools Resource)
 NEMAR is a curated repository for neurophysiology data in BIDS format.
 This CLI provides tools for uploading, downloading, and managing datasets.`).version(vJ,"-v, --version","Output the current version").option("--no-color","Disable colored output").option("--verbose","Enable verbose output").option("--help-all","Show detailed help with examples and descriptions").addHelpText("after",`