@precisionutilityguild/liquid-shadow 1.0.9 → 1.0.11

package/dist/entry/ember/index.js

@@ -1,96 +1,73 @@
-var at=Object.defineProperty;var P=(s,e)=>()=>(s&&(e=s(s=0)),e);var lt=(s,e)=>{for(var t in e)at(s,t,{get:e[t],enumerable:!0})};import ct from"pino";var ut,dt,d,M=P(()=>{"use strict";ut={10:"TRACE",20:"DEBUG",30:"INFO",40:"WARN",50:"ERROR",60:"FATAL"},dt=ct({level:process.env.LOG_LEVEL||"warn",base:{service:"liquid-shadow"},formatters:{level(s,e){return{level:s,severity:ut[e]??"INFO"}}},transport:{target:"pino-pretty",options:{colorize:!0,translateTime:"HH:MM:ss",destination:2,levelKey:"severity",messageKey:"message"}}}),d=dt});import{fileURLToPath as xt}from"node:url";import{dirname as le,join as Me,resolve as wt}from"node:path";import{existsSync as kt}from"node:fs";function Wt(){let s=Ce;for(;s!==le(s);){if(kt(Me(s,"package.json")))return s;s=le(s)}return wt(Ce,"..","..")}function De(...s){return Me(Wt(),...s)}var Ft,Ce,Ae=P(()=>{"use strict";Ft=xt(import.meta.url),Ce=le(Ft)});import{Worker as Ht}from"node:worker_threads";import{cpus as vt}from"node:os";import{fileURLToPath as Bt}from"node:url";import{dirname as Ut,join as xe}from"node:path";import{existsSync as we}from"node:fs";function Pt(){if(Fe.endsWith(".ts")){let e=xe(ke,"worker.ts");if(we(e))return e}let s=xe(ke,"worker.js");return we(s)?s:De("dist/logic/domain/embeddings/worker.js")}function x(s){return A||(A=new W(s)),A}async function We(){A&&(await A.shutdown(),A=null)}var Fe,ke,W,A,He=P(()=>{"use strict";M();Ae();Fe=Bt(import.meta.url),ke=Ut(Fe);W=class{workers=[];taskQueue=[];pendingTasks=new Map;taskIdCounter=0;initialized=!1;initPromise;shutdownRequested=!1;numWorkers;cacheDir;initTimeout;constructor(e={}){this.numWorkers=e.numWorkers??Math.max(1,Math.min(2,vt().length-1)),this.cacheDir=e.cacheDir??"./.cache",this.initTimeout=e.initTimeout??6e4}async initialize(){if(!this.initialized)return this.initPromise?this.initPromise:(this.initPromise=this._doInitialize(),this.initPromise)}async _doInitialize(){let e;try{d.info({numWorkers:this.numWorkers},"Initializing embedding worker pool");let t=new 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Promise(i=>{t.worker.postMessage({type:"shutdown"}),t.worker.once("exit",()=>i()),setTimeout(()=>{t.worker.terminate().then(()=>i())},5e3)}));await Promise.all(e),this.workers=[],this.taskQueue=[],this.pendingTasks.clear(),this.initialized=!1,this.shutdownRequested=!1,d.info("Embedding worker pool shutdown complete")}},A=null});var I={};lt(I,{EmbeddingPriorityQueue:()=>ue,EmbeddingWorkerPool:()=>W,cosineSimilarity:()=>qt,generateEmbedding:()=>Kt,generateEmbeddingsBatch:()=>jt,getDefaultPool:()=>x,setUseWorkerThreads:()=>zt,shutdownDefaultPool:()=>We});async function $t(){return H||(H=await import("@xenova/transformers"),H.env.cacheDir="./.cache",H.env.allowLocalModels=!0),H}function zt(s){de=s,d.info({useWorkerThreads:s},"Worker thread mode updated")}function ve(s=!1){let e=(v||"").toLowerCase(),t={};return v&&(t.dtype=v),s?(t.quantized=!1,t):(e==="fp32"||e==="fp16"||e==="float32"||e==="float16"?t.quantized=!1:e.startsWith("q")&&(t.quantized=!0),t)}async function Yt(){d.info({model:G,dtype:v},"Loading embedding model...");let{pipeline:s}=await $t(),e=ve(!1);try{return await s("feature-extraction",G,e)}catch(t){let i=t?.message||"";if(!(i.includes("/onnx/model_quantized.onnx")||i.includes("model_quantized.onnx")))throw t;return d.warn({model:G,dtype:v},"Quantized ONNX artifact missing, retrying with unquantized ONNX"),await s("feature-extraction",G,ve(!0))}}async function Ue(){return ce||(ce=Yt()),ce}async function Kt(s){try{let t=await(await Ue())(s,{pooling:"mean",normalize:!0});return Array.from(t.data)}catch(e){return d.error({err:e},"Failed to generate embedding"),null}}async function jt(s,e=Be,t){return s.length===0?[]:de?x().generateEmbeddings(s,e,t):Pe(s,e,t)}async function Pe(s,e,t){let i=new Array(s.length).fill(null),n=await Ue();for(let r=0;r<s.length;r+=e){let c=Math.min(r+e,s.length),l=s.slice(r,c);try{let a=await n(l,{pooling:"mean",normalize:!0}),[o,u]=a.dims;for(let m=0;m<o;m++){let 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from"fs";import $ from"path";import{fileURLToPath as mt}from"url";var R=d.child({module:"migrations"}),pt=mt(import.meta.url),Et=$.dirname(pt);function ht(){let s=Et;if(O.readdirSync(s).some(i=>i.match(/^\d{3}_.*\.sql$/)))return s;let t=$.resolve(s,"../../data/migrations");return O.existsSync(t)&&O.readdirSync(t).some(i=>i.match(/^\d{3}_.*\.sql$/))?t:s}function ft(s){s.exec(`
+var at=Object.defineProperty;var P=(s,e)=>()=>(s&&(e=s(s=0)),e);var lt=(s,e)=>{for(var t in e)at(s,t,{get:e[t],enumerable:!0})};import ct from"pino";var ut,dt,d,A=P(()=>{"use strict";ut={10:"TRACE",20:"DEBUG",30:"INFO",40:"WARN",50:"ERROR",60:"FATAL"},dt=ct({level:process.env.LOG_LEVEL||"warn",base:{service:"liquid-shadow"},formatters:{level(s,e){return{level:s,severity:ut[e]??"INFO"}}},transport:{target:"pino-pretty",options:{colorize:!0,translateTime:"HH:MM:ss",destination:2,levelKey:"severity",messageKey:"message"}}}),d=dt});import{existsSync as xt}from"node:fs";import{dirname as le,join as Ae,resolve as kt}from"node:path";import{fileURLToPath as wt}from"node:url";function Wt(){let s=Ce;for(;s!==le(s);){if(xt(Ae(s,"package.json")))return s;s=le(s)}return kt(Ce,"..","..")}function De(...s){return Ae(Wt(),...s)}var Ft,Ce,Me=P(()=>{"use strict";Ft=wt(import.meta.url),Ce=le(Ft)});import{existsSync as xe}from"node:fs";import{cpus as Ht}from"node:os";import{dirname as vt,join as ke}from"node:path";import{fileURLToPath as Ut}from"node:url";import{Worker as Bt}from"node:worker_threads";function Pt(){if(Fe.endsWith(".ts")){let e=ke(we,"worker.ts");if(xe(e))return e}let s=ke(we,"worker.js");return xe(s)?s:De("dist/logic/domain/embeddings/worker.js")}function x(s){return M||(M=new W(s)),M}async function We(){M&&(await M.shutdown(),M=null)}var Fe,we,W,M,He=P(()=>{"use strict";Me();A();Fe=Ut(import.meta.url),we=vt(Fe);W=class{workers=[];taskQueue=[];pendingTasks=new Map;taskIdCounter=0;initialized=!1;initPromise;shutdownRequested=!1;numWorkers;cacheDir;initTimeout;constructor(e={}){this.numWorkers=e.numWorkers??Math.max(1,Math.min(2,Ht().length-1)),this.cacheDir=e.cacheDir??"./.cache",this.initTimeout=e.initTimeout??6e4}async initialize(){if(!this.initialized)return this.initPromise?this.initPromise:(this.initPromise=this._doInitialize(),this.initPromise)}async _doInitialize(){let e;try{d.info({numWorkers:this.numWorkers},"Initializing embedding worker pool");let t=new Promise((i,n)=>{e=setTimeout(()=>n(new Error(`Worker pool initialization timed out after ${this.initTimeout}ms`)),this.initTimeout)});if(await Promise.race([this._initializeWorkers(),t]),e&&clearTimeout(e),this.shutdownRequested){this.initialized=!1,this.initPromise=void 0,d.debug("Initialization completed but shutdown was requested");return}this.initialized=!0,d.info({numWorkers:this.workers.length},"Embedding worker pool ready")}catch(t){throw e&&clearTimeout(e),this.initPromise=void 0,this.initialized=!1,await this.shutdown(),t}}async _initializeWorkers(){let e=Pt();d.debug({workerPath:e},"Resolved worker path");let t=[];for(let i=0;i<this.numWorkers;i++)i>0&&await new Promise(n=>setTimeout(n,25)),t.push(this.createWorker(e,i));await Promise.all(t)}async createWorker(e,t){return new Promise((i,n)=>{let r=setTimeout(()=>{n(new Error(`Worker ${t} initialization timed out`))},this.initTimeout),c=new Bt(e,{workerData:{cacheDir:this.cacheDir},execArgv:process.execArgv}),l={worker:c,busy:!1,currentTaskId:null};c.on("message",a=>{if(a.type==="ready"){if(clearTimeout(r),this.shutdownRequested){d.debug({workerIndex:t},"Worker ready but shutdown requested, terminating"),c.terminate().catch(()=>{}),i();return}this.workers.push(l),d.debug({workerIndex:t},"Worker ready"),i()}else a.type==="result"&&a.id?this.handleTaskComplete(l,a.id,a.embeddings||[]):a.type==="error"&&a.id&&this.handleTaskError(l,a.id,new Error(a.error||"Unknown error"))}),c.on("error",a=>{if(clearTimeout(r),d.error({err:a,workerIndex:t},"Worker error"),l.currentTaskId&&this.handleTaskError(l,l.currentTaskId,a),!this.initialized){n(a);return}let o=this.workers.indexOf(l);o!==-1&&this.workers.splice(o,1),!this.shutdownRequested&&this.initialized&&this.createWorker(e,t).catch(u=>{d.error({err:u},"Failed to replace crashed worker")})}),c.on("exit",a=>{a!==0&&!this.shutdownRequested&&d.warn({workerIndex:t,code:a},"Worker exited unexpectedly")})})}handleTaskComplete(e,t,i){let n=this.pendingTasks.get(t);n&&(this.pendingTasks.delete(t),n.resolve(i)),e.busy=!1,e.currentTaskId=null,this.processQueue()}handleTaskError(e,t,i){let n=this.pendingTasks.get(t);n&&(this.pendingTasks.delete(t),n.reject(i)),e.busy=!1,e.currentTaskId=null,this.processQueue()}processQueue(){if(this.taskQueue.length===0)return;let e=this.workers.find(i=>!i.busy);if(!e)return;let t=this.taskQueue.shift();t&&(e.busy=!0,e.currentTaskId=t.id,this.pendingTasks.set(t.id,t),e.worker.postMessage({type:"embed",id:t.id,texts:t.texts}))}async generateEmbeddings(e,t=128,i){if(this.initialized||await this.initialize(),e.length===0)return[];let n=[];for(let o=0;o<e.length;o+=t)n.push(e.slice(o,o+t));let r=new Array(n.length),c=0,l=n.map((o,u)=>new Promise((m,p)=>{let g={id:`task_${++this.taskIdCounter}`,texts:o,resolve:T=>{if(r[u]=T,c++,i){let N=Math.min(c*t,e.length);i(N,e.length)}m()},reject:T=>{if(r[u]=new Array(o.length).fill(null),c++,d.warn({err:T,chunkIndex:u},"Chunk embedding failed"),i){let N=Math.min(c*t,e.length);i(N,e.length)}m()}};this.taskQueue.push(g),this.processQueue()}));await Promise.all(l);let a=[];for(let o of r)a.push(...o);return d.info({total:e.length,successful:a.filter(o=>o!==null).length,workers:this.workers.length},"Parallel embedding generation complete"),a}get workerCount(){return this.workers.length}get busyWorkers(){return this.workers.filter(e=>e.busy).length}get queueSize(){return this.taskQueue.length}get isInitialized(){return this.initialized}async shutdown(){if(this.shutdownRequested=!0,this.initPromise)try{await this.initPromise}catch{}if(!this.initialized&&this.workers.length===0){this.shutdownRequested=!1,this.initPromise=void 0;return}d.info({numWorkers:this.workers.length},"Shutting down embedding worker pool");let e=this.workers.map(t=>new Promise(i=>{t.worker.postMessage({type:"shutdown"}),t.worker.once("exit",()=>i()),setTimeout(()=>{t.worker.terminate().then(()=>i())},5e3)}));await Promise.all(e),this.workers=[],this.taskQueue=[],this.pendingTasks.clear(),this.initialized=!1,this.shutdownRequested=!1,d.info("Embedding worker pool shutdown complete")}},M=null});var O={};lt(O,{EmbeddingPriorityQueue:()=>ue,EmbeddingWorkerPool:()=>W,cosineSimilarity:()=>jt,generateEmbedding:()=>Yt,generateEmbeddingsBatch:()=>qt,getDefaultPool:()=>x,setUseWorkerThreads:()=>zt,shutdownDefaultPool:()=>We});async function $t(){return H||(H=await import("@xenova/transformers"),H.env.cacheDir="./.cache",H.env.allowLocalModels=!0),H}function zt(s){de=s,d.info({useWorkerThreads:s},"Worker thread mode updated")}function ve(s=!1){let e=(v||"").toLowerCase(),t={};return v&&(t.dtype=v),s?(t.quantized=!1,t):(e==="fp32"||e==="fp16"||e==="float32"||e==="float16"?t.quantized=!1:e.startsWith("q")&&(t.quantized=!0),t)}async function Kt(){d.info({model:X,dtype:v},"Loading embedding model...");let{pipeline:s}=await $t(),e=ve(!1);try{return await s("feature-extraction",X,e)}catch(t){let i=t?.message||"";if(!(i.includes("/onnx/model_quantized.onnx")||i.includes("model_quantized.onnx")))throw t;return d.warn({model:X,dtype:v},"Quantized ONNX artifact missing, retrying with unquantized ONNX"),await s("feature-extraction",X,ve(!0))}}async function Be(){return ce||(ce=Kt()),ce}async function Yt(s){try{let t=await(await Be())(s,{pooling:"mean",normalize:!0});return Array.from(t.data)}catch(e){return d.error({err:e},"Failed to generate embedding"),null}}async function qt(s,e=Ue,t){return s.length===0?[]:de?x().generateEmbeddings(s,e,t):Pe(s,e,t)}async function Pe(s,e,t){let i=new Array(s.length).fill(null),n=await Be();for(let r=0;r<s.length;r+=e){let c=Math.min(r+e,s.length),l=s.slice(r,c);try{let a=await n(l,{pooling:"mean",normalize:!0}),[o,u]=a.dims;for(let m=0;m<o;m++){let p=m*u,y=p+u;i[r+m]=Array.from(a.data.slice(p,y))}}catch(a){d.error({err:a,batchStart:r,batchEnd:c},"Single-threaded batch embedding failed, falling back to sequential for this chunk");for(let o=0;o<l.length;o++)try{let u=l[o];if(!u||u.trim().length===0)continue;let m=await n(u,{pooling:"mean",normalize:!0});i[r+o]=Array.from(m.data)}catch{i[r+o]=null}}t&&t(c,s.length)}return d.debug({total:s.length,successful:i.filter(r=>r!==null).length},"Batch embedding complete"),i}function jt(s,e){let t=0,i=0,n=0;for(let r=0;r<s.length;r++)t+=s[r]*e[r],i+=s[r]*s[r],n+=e[r]*e[r];return t/(Math.sqrt(i)*Math.sqrt(n))}var X,v,H,Ue,de,ce,ue,S=P(()=>{"use strict";A();He();X=process.env.EMBEDDING_MODEL??"Xenova/all-MiniLM-L6-v2",v=process.env.EMBEDDING_DTYPE??"fp32",H=null;Ue=128,de=!1;ce=null;ue=class{queue=[];processing=!1;results=new Map;enqueue(e){this.queue.push(e),this.queue.sort((t,i)=>i.priority-t.priority)}enqueueMany(e){this.queue.push(...e),this.queue.sort((t,i)=>i.priority-t.priority)}get size(){return this.queue.length}get isProcessing(){return this.processing}getResult(e){return this.results.get(e)}async processQueue(e=Ue,t){if(this.processing)return d.warn("Queue processing already in progress"),this.results;this.processing=!0;let i=this.queue.length;try{de?await this.processQueueParallel(e,i,t):await this.processQueueSequential(e,i,t)}finally{this.processing=!1}return this.results}async processQueueSequential(e,t,i){for(;this.queue.length>0;){let n=this.queue.splice(0,e),r=n.map(l=>l.text),c=await Pe(r,r.length);if(n.forEach((l,a)=>{this.results.set(l.id,c[a])}),i){let l=t-this.queue.length;i(l,t)}}}async processQueueParallel(e,t,i){let n=this.queue.splice(0),r=n.map(a=>a.text),l=await x().generateEmbeddings(r,e,(a,o)=>{i&&i(a,o)});n.forEach((a,o)=>{this.results.set(a.id,l[o])})}clear(){this.queue=[],this.results.clear()}}});import me from"node:os";A();import Tt from"better-sqlite3";import Rt from"crypto";import Re from"fs";import z from"path";A();import I from"fs";import $ from"path";import{fileURLToPath as mt}from"url";var R=d.child({module:"migrations"}),pt=mt(import.meta.url),Et=$.dirname(pt);function ht(){let s=Et;if(I.readdirSync(s).some(i=>i.match(/^\d{3}_.*\.sql$/)))return s;let t=$.resolve(s,"../../data/migrations");return I.existsSync(t)&&I.readdirSync(t).some(i=>i.match(/^\d{3}_.*\.sql$/))?t:s}function ft(s){s.exec(`
     CREATE TABLE IF NOT EXISTS schema_migrations (
       version    INTEGER PRIMARY KEY,
       name       TEXT    NOT NULL,
       applied_at REAL    DEFAULT (unixepoch())
     );
-  `)}function gt(s){ft(s);let e=s.prepare("SELECT version FROM schema_migrations ORDER BY version").all();return new Set(e.map(t=>t.version))}function _t(s){return O.readdirSync(s).filter(t=>t.match(/^\d{3}_.*\.sql$/)&&!t.startsWith("000_")).sort().map(t=>{let i=t.match(/^(\d{3})_(.+)\.sql$/),n=parseInt(i[1],10),r=i[2],l=O.readFileSync($.join(s,t),"utf-8").split(/^-- DOWN$/m);return{version:n,name:r,up:l[0].trim(),down:l[1]?.trim()}})}function bt(s,e){R.info({version:e.version,name:e.name},"Applying migration"),s.transaction(()=>{s.exec(e.up),s.prepare("INSERT INTO schema_migrations (version, name) VALUES (?, ?)").run(e.version,e.name)})(),R.info({version:e.version},"Migration applied successfully")}function yt(s,e,t){let i=$.join(e,"000_baseline.sql");if(!O.existsSync(i)){R.warn("000_baseline.sql not found \u2014 falling back to incremental migrations");return}R.info("Fresh database detected \u2014 applying consolidated baseline schema");let n=O.readFileSync(i,"utf-8");s.transaction(()=>{s.exec(n);let r=s.prepare("INSERT OR IGNORE INTO schema_migrations (version, name) VALUES (?, ?)");for(let c of t)r.run(c.version,c.name)})(),R.info({stamped:t.length},"Baseline applied \u2014 incremental migrations stamped")}function Te(s){let e=gt(s),t=ht(),i=_t(t);if(e.size===0){yt(s,t,i);return}let n=i.filter(r=>!e.has(r.version));if(n.length===0){R.debug("No pending migrations");return}R.info({count:n.length},"Running pending migrations");for(let r of n)bt(s,r);R.info("All migrations complete")}import St from"os";var D=d.child({module:"db"});function oe(s){let e=St.homedir(),t=z.join(e,".mcp-liquid-shadow"),i=z.join(t,"dbs");Re.existsSync(i)||Re.mkdirSync(i,{recursive:!0});let n=Rt.createHash("sha256").update(s).digest("hex").substring(0,12),c=`${z.basename(s).replace(/[^a-zA-Z0-9-_]/g,"_")}_${n}.db`;return z.join(i,c)}function Lt(s,e){let t=e||oe(s);D.debug({repoPath:s,dbPath:t},"Initializing database");let i=new Tt(t);return i.pragma("journal_mode = WAL"),i.pragma("busy_timeout = 5000"),Te(i),Y.set(s,t),S.set(t,i),D.debug({repoPath:s,dbPath:t},"Database initialized successfully"),i}var S=new Map,Y=new Map;function F(s){let e=Y.get(s)||oe(s),t=S.get(e);if(t){if(t.open)return t;S.delete(e)}let i=Lt(s);return S.set(e,i),i}function Se(s){let e=Y.get(s)||oe(s),t=S.get(e);t&&(t.open&&(D.debug({repoPath:s,dbPath:e},"Closing database connection"),t.close()),S.delete(e)),Y.delete(s)}function Le(){for(let[s,e]of S.entries())try{e.open&&(D.debug({dbPath:s},"Closing database connection"),e.close())}catch(t){D.error({dbPath:s,err:t},"Error closing database execution")}S.clear()}process.on("exit",()=>Le());var Ne=s=>{D.debug({signal:s},"Received termination signal, closing databases"),Le(),process.exit(0)};process.on("SIGINT",()=>Ne("SIGINT"));process.on("SIGTERM",()=>Ne("SIGTERM"));import At from"path";var E=class{db;constructor(e){this.db=e}get database(){return this.db}all(e,...t){return this.db.prepare(e).all(...t)}get(e,...t){return this.db.prepare(e).get(...t)}run(e,...t){return this.db.prepare(e).run(...t).changes}insert(e,...t){return this.db.prepare(e).run(...t).lastInsertRowid}transaction(e){return this.db.transaction(e)()}};var Nt=new Set(["any","unknown","never","void","null","undefined","string","number","boolean","symbol","object","bigint","readonly","keyof","infer","extends","implements","class","interface","type","function","new"]);function Ot(s,e){if(!s)return!1;let t=s.trim();return!t||Nt.has(t.toLowerCase())||e.has(t)?!1:/^[A-Za-z_$][A-Za-z0-9_$.]*$/.test(t)}function It(s){return s.split(/[,|&]/).map(e=>e.trim()).filter(Boolean)}function Ct(s){let e=s.replace(/^[({\[]+/,"").replace(/[)}\]]+$/,"").replace(/^readonly\s+/,"").trim();return e&&e.match(/^([A-Za-z_$][A-Za-z0-9_$.]*)/)?.[1]||null}function Mt(s){let e=[],t=0,i="",n=!1;for(let r of s){if(r==="<"&&(t++,t===1)){n=!0,i="";continue}if(r===">"&&(t>0&&t--,t===0&&n)){n=!1,i.trim()&&e.push(i),i="";continue}n&&(i+=r)}return e}function Dt(s){let e=new Set;for(let t of s){let i=t.split(",").map(n=>n.trim());for(let n of i){let r=n.match(/^([A-Za-z_$][A-Za-z0-9_$]*)/);r?.[1]&&e.add(r[1])}}return e}function ae(s,e){let t=[];for(let i of It(s)){let n=Ct(i);n&&Ot(n,e)&&t.push(n)}return t}function Oe(s){if(!s)return[];let e=s.replace(/\s+/g," ").trim();if(!e)return[];let t=Mt(e),i=Dt(t),n=[],r=new Set,c=(o,u,m)=>{let p=`${o}:${u}`;r.has(p)||(r.add(p),n.push({relationship:o,targetName:u,...m?{metadata:m}:{}}))},l=e.match(/\bextends\s+(.+?)(?=\bimplements\b|\{|=|$)/);if(l?.[1]){let o=ae(l[1],i);for(let u of o)c("extends",u,l[1].trim())}let a=e.match(/\bimplements\s+(.+?)(?=\{|=|$)/);if(a?.[1]){let o=ae(a[1],i);for(let u of o)c("implements",u,a[1].trim())}for(let o of t){let u=/([A-Za-z_$][A-Za-z0-9_$]*)\s+extends\s+([^,>]+)/g,m=null;for(;(m=u.exec(o))!==null;){let p=m[2]?.trim();if(!p)continue;let y=ae(p,i);for(let g of y)c("constrained_by",g,p)}}return n}var K=class extends E{findByPath(e){return this.get("SELECT * FROM files WHERE path = ?",e)}findAll(e){let t="SELECT * FROM files ORDER BY path ASC";return e&&(t+=` LIMIT ${e}`),this.all(t)}getAllPaths(){return this.all("SELECT path FROM files").map(t=>t.path)}findInSubPath(e,t){let i=At.resolve(e,t),n=i.endsWith("/")?i:i+"/";return this.all(`
-      SELECT * FROM files 
-      WHERE (path LIKE ? OR path = ?)
-      ORDER BY path ASC
-    `,`${n}%`,i)}findWithEmbeddings(){return this.all("SELECT * FROM files WHERE embedding IS NOT NULL")}findFts(e,t=10){return this.all(`
-      SELECT files.*, files_fts.rank
-      FROM files_fts
-      JOIN files ON files.rowid = files_fts.rowid
-      WHERE files_fts MATCH ?
-      ORDER BY rank
-      LIMIT ?
-    `,e,t)}findByPathKeywords(e,t=10){let i=e.map(()=>"LOWER(path) LIKE ?").join(" OR ");return this.all(`
-      SELECT * FROM files 
-      WHERE ${i}
-      LIMIT ?
-    `,...e.map(n=>`%${n}%`),t)}findContentFts(e,t=50){let i=this.buildContentFtsQuery(e);return i?this.all(`
+  `)}function gt(s){ft(s);let e=s.prepare("SELECT version FROM schema_migrations ORDER BY version").all();return new Set(e.map(t=>t.version))}function _t(s){return I.readdirSync(s).filter(t=>t.match(/^\d{3}_.*\.sql$/)&&!t.startsWith("000_")).sort().map(t=>{let i=t.match(/^(\d{3})_(.+)\.sql$/),n=parseInt(i[1],10),r=i[2],l=I.readFileSync($.join(s,t),"utf-8").split(/^-- DOWN$/m);return{version:n,name:r,up:l[0].trim(),down:l[1]?.trim()}})}function bt(s,e){R.info({version:e.version,name:e.name},"Applying migration"),s.transaction(()=>{s.exec(e.up),s.prepare("INSERT INTO schema_migrations (version, name) VALUES (?, ?)").run(e.version,e.name)})(),R.info({version:e.version},"Migration applied successfully")}function yt(s,e,t){let i=$.join(e,"000_baseline.sql");if(!I.existsSync(i)){R.warn("000_baseline.sql not found \u2014 falling back to incremental migrations");return}R.info("Fresh database detected \u2014 applying consolidated baseline schema");let n=I.readFileSync(i,"utf-8");s.transaction(()=>{s.exec(n);let r=s.prepare("INSERT OR IGNORE INTO schema_migrations (version, name) VALUES (?, ?)");for(let c of t)r.run(c.version,c.name)})(),R.info({stamped:t.length},"Baseline applied \u2014 incremental migrations stamped")}function Te(s){let e=gt(s),t=ht(),i=_t(t);if(e.size===0){yt(s,t,i);return}let n=i.filter(r=>!e.has(r.version));if(n.length===0){R.debug("No pending migrations");return}R.info({count:n.length},"Running pending migrations");for(let r of n)bt(s,r);R.info("All migrations complete")}import Lt from"os";var D=d.child({module:"db"});function oe(s){let e=Lt.homedir(),t=z.join(e,".mcp-liquid-shadow"),i=z.join(t,"dbs");Re.existsSync(i)||Re.mkdirSync(i,{recursive:!0});let n=Rt.createHash("sha256").update(s).digest("hex").substring(0,12),c=`${z.basename(s).replace(/[^a-zA-Z0-9-_]/g,"_")}_${n}.db`;return z.join(i,c)}function St(s,e){let t=e||oe(s);D.debug({repoPath:s,dbPath:t},"Initializing database");let i=new Tt(t);return i.pragma("journal_mode = WAL"),i.pragma("busy_timeout = 5000"),Te(i),K.set(s,t),L.set(t,i),D.debug({repoPath:s,dbPath:t},"Database initialized successfully"),i}var L=new Map,K=new Map;function F(s){let e=K.get(s)||oe(s),t=L.get(e);if(t){if(t.open)return t;L.delete(e)}let i=St(s);return L.set(e,i),i}function Le(s){let e=K.get(s)||oe(s),t=L.get(e);t&&(t.open&&(D.debug({repoPath:s,dbPath:e},"Closing database connection"),t.close()),L.delete(e)),K.delete(s)}function Se(){for(let[s,e]of L.entries())try{e.open&&(D.debug({dbPath:s},"Closing database connection"),e.close())}catch(t){D.error({dbPath:s,err:t},"Error closing database execution")}L.clear()}process.on("exit",()=>Se());var Ne=s=>{D.debug({signal:s},"Received termination signal, closing databases"),Se(),process.exit(0)};process.on("SIGINT",()=>Ne("SIGINT"));process.on("SIGTERM",()=>Ne("SIGTERM"));var E=class{db;constructor(e){this.db=e}get database(){return this.db}all(e,...t){return this.db.prepare(e).all(...t)}get(e,...t){return this.db.prepare(e).get(...t)}run(e,...t){return this.db.prepare(e).run(...t).changes}insert(e,...t){return this.db.prepare(e).run(...t).lastInsertRowid}transaction(e){return this.db.transaction(e)()}};var Y=class extends E{claimFile(e,t){try{this.run(`
+        INSERT INTO file_claims (file_path, mission_id, claimed_at, updated_at)
+        VALUES (?, ?, unixepoch(), unixepoch())
+      `,e,t);let i=this.getClaim(e);if(!i)throw new Error(`Failed to hydrate claim after insert for file ${e}`);return{status:"claimed",claim:i}}catch{let i=this.getClaim(e);if(!i)throw new Error(`Failed to read existing claim for file ${e}`);return i.mission_id===t?(this.run("UPDATE file_claims SET updated_at = unixepoch() WHERE file_path = ?",e),{status:"already_claimed",claim:this.getClaim(e)??i}):{status:"conflict",claim:i}}}releaseFile(e,t){let i=this.getClaim(e);return i?t!==void 0&&i.mission_id!==t?{released:!1,reason:"not_owner",claim:i}:(this.run("DELETE FROM file_claims WHERE file_path = ?",e),{released:!0}):{released:!1,reason:"not_found"}}releaseAllForMission(e){return this.run("DELETE FROM file_claims WHERE mission_id = ?",e)}getClaim(e){return this.get(`
       SELECT
-        files.*,
-        bm25(content_fts, 0.2, 1.0) AS bm25_rank
+        fc.file_path,
+        fc.mission_id,
+        fc.claimed_at,
+        fc.updated_at,
+        m.name AS mission_name,
+        m.status AS mission_status,
+        m.git_branch AS mission_branch
+      FROM file_claims fc
+      LEFT JOIN missions m ON m.id = fc.mission_id
+      WHERE fc.file_path = ?
+    `,e)}getClaimsForMission(e){return this.all(`
+      SELECT
+        fc.file_path,
+        fc.mission_id,
+        fc.claimed_at,
+        fc.updated_at,
+        m.name AS mission_name,
+        m.status AS mission_status,
+        m.git_branch AS mission_branch
+      FROM file_claims fc
+      LEFT JOIN missions m ON m.id = fc.mission_id
+      WHERE fc.mission_id = ?
+      ORDER BY fc.file_path ASC
+    `,e)}listClaims(){return this.all(`
+      SELECT
+        fc.file_path,
+        fc.mission_id,
+        fc.claimed_at,
+        fc.updated_at,
+        m.name AS mission_name,
+        m.status AS mission_status,
+        m.git_branch AS mission_branch
+      FROM file_claims fc
+      LEFT JOIN missions m ON m.id = fc.mission_id
+      ORDER BY fc.updated_at DESC, fc.file_path ASC
+    `)}getClaimsByFiles(e){if(e.length===0)return[];let t=e.map(()=>"?").join(", ");return this.all(`
+      SELECT
+        fc.file_path,
+        fc.mission_id,
+        fc.claimed_at,
+        fc.updated_at,
+        m.name AS mission_name,
+        m.status AS mission_status,
+        m.git_branch AS mission_branch
+      FROM file_claims fc
+      LEFT JOIN missions m ON m.id = fc.mission_id
+      WHERE fc.file_path IN (${t})
+      ORDER BY fc.file_path ASC
+    `,...e)}};var q=class extends E{findByKey(e,t=20){return this.all(`
+      SELECT file_path, key, value, kind
+      FROM configs
+      WHERE key LIKE ? OR value LIKE ?
+      LIMIT ?
+      `,`%${e}%`,`%${e}%`,t)}findByKind(e,t=50){let i="SELECT key, value, kind, file_path FROM configs",n=[];return e&&(i+=" WHERE kind = ?",n.push(e)),i+=" LIMIT ?",n.push(t),this.all(i,...n)}findEnvValue(e){return this.get("SELECT value FROM configs WHERE key LIKE ? OR key = ? LIMIT 1",`%:env:${e}`,e)?.value}countByKind(e){return this.get("SELECT COUNT(*) as count FROM configs WHERE kind = ?",e)?.count||0}getAll(){return this.all("SELECT key, value, kind, file_path FROM configs")}};var j=class extends E{search(e,t=10){return this.all(`
+      SELECT file_path, snippet(content_fts, 1, '<b>', '</b>', '...', 20) as snippet
       FROM content_fts
-      JOIN files ON files.path = content_fts.file_path
       WHERE content_fts MATCH ?
-      ORDER BY bm25_rank ASC
       LIMIT ?
-    `,i,Math.max(1,Math.min(t,1e3))):[]}getContent(e){return this.get("SELECT content FROM file_content WHERE file_path = ?",e)?.content}findContentByToken(e,t=10){return this.all(`
-          SELECT file_path 
-          FROM content_fts 
-          WHERE content_fts MATCH ? 
-            AND (file_path LIKE '%.ts' OR file_path LIKE '%.tsx' OR file_path LIKE '%.js' OR file_path LIKE '%.py' OR file_path LIKE '%.php')
-            AND file_path NOT LIKE '%/test/%'
-            AND file_path NOT LIKE '%.spec.%'
-          LIMIT ?
-        `,`"${e.replace(/[^a-zA-Z0-9_\/]/g," ")}"`,t).map(n=>n.file_path)}findSynapses(e){let t="SELECT * FROM event_synapses WHERE 1=1",i=[];if(e.type&&(t+=" AND type = ?",i.push(e.type)),e.name){let n=e.name;n.startsWith("/")&&(n=n.substring(1)),n.endsWith("/")&&(n=n.substring(0,n.length-1)),n.length>0&&(t+=" AND (name LIKE ? OR name LIKE ? OR name = ?)",i.push(`${n}%`),i.push(`%/${n}%`),i.push(e.name))}return e.direction&&(t+=" AND direction = ?",i.push(e.direction)),t+=` LIMIT ${e.limit||50}`,this.all(t,...i)}exists(e){return!!this.get("SELECT 1 FROM files WHERE path = ?",e)}update(e,t){let i=Object.keys(t);if(i.length===0)return;let n=i.map(c=>`${c} = ?`).join(", "),r=Object.values(t);r.push(e),this.run(`UPDATE files SET ${n} WHERE path = ?`,...r)}getStats(){let e=this.get(`
-      SELECT
-        COUNT(*) as total,
-        SUM(CASE WHEN summary IS NOT NULL AND summary != '' THEN 1 ELSE 0 END) as withSummary
-      FROM files
-    `);return{total:e?.total||0,withSummary:e?.withSummary||0}}getGravityMap(e=[],t){let i={},n=`
-      SELECT ws.file_path, m.name as mission_name, m.status
-      FROM working_set ws
-      JOIN missions m ON ws.mission_id = m.id
-      WHERE (
-        (m.status IN ('in-progress', 'verifying') ${t?"AND m.git_branch = ?":""})
-        OR m.id IN (${e.length>0?e.join(","):"-1"})
-      )
-      AND ws.file_path IS NOT NULL
-    `,r=[];t&&r.push(t);let c=this.all(n,...r);for(let o of c){i[o.file_path]||(i[o.file_path]={score:1,reasons:[]});let u=o.status==="in-progress"||o.status==="verifying"?1:.5;i[o.file_path].score+=u;let m=o.status==="in-progress"||o.status==="verifying"?"Working Set":"Lineage Bleed";i[o.file_path].reasons.push(`${m}: ${o.mission_name}`)}let l=Math.floor(Date.now()/1e3)-86400,a=this.all(`
-      SELECT file_path, type, mission_id
-      FROM intent_logs
-      WHERE (created_at > ? OR mission_id IN (${e.length>0?e.join(","):"-1"}))
-      AND file_path IS NOT NULL
-      ORDER BY created_at DESC
-      LIMIT 100
-    `,l);for(let o of a){i[o.file_path]||(i[o.file_path]={score:1,reasons:[]});let u=o.mission_id?e.includes(o.mission_id):!1,m=u?.1:.2;i[o.file_path].score<5&&(i[o.file_path].score+=m);let p=u?`Lineage Intent: ${o.type}`:`Recent Intent: ${o.type}`;!i[o.file_path].reasons.includes(p)&&i[o.file_path].reasons.length<5&&i[o.file_path].reasons.push(p)}return i}getCount(){return this.get("SELECT COUNT(*) as count FROM files")?.count||0}getTopDirectories(e,t=8){return this.all(`
-        SELECT 
-            SUBSTR(path, LENGTH(?) + 2, 
-                INSTR(SUBSTR(path, LENGTH(?) + 2), '/') - 1
-            ) as root,
-            COUNT(*) as total_files,
-            SUM(CASE 
-                WHEN path LIKE '%.ts' OR path LIKE '%.tsx' 
-                  OR path LIKE '%.js' OR path LIKE '%.jsx' 
-                  OR path LIKE '%.mjs' OR path LIKE '%.cjs' 
-                THEN 1 ELSE 0 
-            END) as ts_files
-        FROM files 
-        WHERE path LIKE ? || '/%/%'
-        GROUP BY root
-        ORDER BY total_files DESC
-        LIMIT ?
-    `,e,e,e,t)}hasFilesPattern(e){return!!this.get("SELECT 1 FROM files WHERE path LIKE ? LIMIT 1",e)}findPackageJsonChildren(e){return this.all(`
-        SELECT
-            path,
-            SUBSTR(path, LENGTH(?) + 2) as relPath
-        FROM files
-        WHERE path LIKE ? || '/%/package.json'
-    `,e,e)}deletePaths(e){if(e.length===0)return;let t=this.db.prepare("DELETE FROM files WHERE path = ?");this.db.transaction(n=>{for(let r of n)t.run(r)})(e)}updateMtime(e,t){this.run("UPDATE files SET mtime = ? WHERE path = ?",t,e)}batchSaveIndexResults(e,t,i,n){let r=this.db.prepare("DELETE FROM exports WHERE file_path = ?"),c=this.db.prepare("DELETE FROM imports WHERE file_path = ?"),l=this.db.prepare("DELETE FROM configs WHERE file_path = ?"),a=this.db.prepare("DELETE FROM file_content WHERE file_path = ?"),o=this.db.prepare("DELETE FROM event_synapses WHERE file_path = ?"),u=this.db.prepare("DELETE FROM type_graph_edges WHERE file_path = ?"),m=this.db.prepare("INSERT INTO exports (file_path, name, kind, signature, doc, start_line, end_line, classification, capabilities, parent_id, embedding) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)"),p=this.db.prepare("INSERT INTO imports (file_path, module_specifier, imported_symbols, resolved_path) VALUES (?, ?, ?, ?)"),y=this.db.prepare("INSERT INTO configs (file_path, key, value, kind) VALUES (?, ?, ?, ?)"),g=this.db.prepare("INSERT INTO file_content (file_path, content) VALUES (?, ?)"),T=this.db.prepare("INSERT INTO event_synapses (file_path, type, name, direction, line_number, code_snippet) VALUES (?, ?, ?, ?, ?, ?)"),N=this.db.prepare("INSERT INTO type_graph_edges (file_path, source_symbol_id, source_symbol_name, target_symbol_name, relationship, line_number, metadata) VALUES (?, ?, ?, ?, ?, ?, ?)"),Je=this.db.prepare(`
-        INSERT INTO files (path, mtime, last_scanned_at, classification, summary, embedding, content_hash)
-        VALUES (?, ?, ?, ?, ?, ?, ?)
-        ON CONFLICT(path) DO UPDATE SET
-            mtime=excluded.mtime,
-            last_scanned_at=excluded.last_scanned_at,
-            classification=excluded.classification,
-            summary=excluded.summary,
-            embedding=excluded.embedding,
-            content_hash=excluded.content_hash
-    `),Qe=this.db.transaction(C=>{for(let Xe of C){let{meta:_,exports:Ee,imports:he,configs:fe,events:ge,content:B,classification:Ze,summary:et,embedding:_e,contentHash:tt}=Xe;r.run(_.path),c.run(_.path),l.run(_.path),a.run(_.path),o.run(_.path),u.run(_.path);let it=tt??(B&&i?i(B):null);if(Je.run(_.path,_.mtime,Date.now(),Ze||"Unknown",et||"",_e?JSON.stringify(_e):null,it),Ee){let h=(k,nt,st)=>{for(let f of nt){let rt=f.embedding?JSON.stringify(f.embedding):null,be=m.run(k,f.name,f.kind,f.signature,f.doc||"",f.line,f.endLine||f.line,f.classification||"Other",f.capabilities||"[]",st,rt),ye=Number(be.lastInsertRowid);if(Number.isFinite(ye)){let ot=Oe(f.signature);for(let U of ot)U.targetName!==f.name&&N.run(k,ye,f.name,U.targetName,U.relationship,f.line,U.metadata||null)}f.members&&f.members.length>0&&h(k,f.members,be.lastInsertRowid)}};h(_.path,Ee,null)}if(he)for(let h of he){let k=h.resolved_path!==void 0?h.resolved_path:n?.(h.module,_.path,t)??"";p.run(_.path,h.module,h.name,k)}if(fe)for(let h of fe)y.run(_.path,h.key,h.value,h.kind);if(B!==void 0&&g.run(_.path,B),ge)for(let h of ge)T.run(_.path,h.type,h.name,h.direction,h.line,h.snippet)}}),pe=500;for(let C=0;C<e.length;C+=pe)Qe(e.slice(C,C+pe))}getLatestScanTime(){return this.get("SELECT MAX(last_scanned_at) as t FROM files")?.t||null}buildContentFtsQuery(e){let t=e.replace(/([a-z0-9])([A-Z])/g,"$1 $2").toLowerCase().split(/[^a-z0-9_]+/).map(r=>r.trim()).filter(r=>r.length>=2).slice(0,12);if(t.length===0)return"";if(t.length===1)return`${t[0]}*`;let i=`"${t.join(" ")}"`,n=t.map(r=>`${r}*`).join(" OR ");return`${i} OR ${n}`}};var j=class s extends E{static HTTP_METHOD_EXPORTS=new Set(["GET","POST","PUT","PATCH","DELETE","HEAD","OPTIONS"]);findByNameAndFile(e,t){return this.all("SELECT * FROM exports WHERE file_path = ? AND name = ?",t,e)}findByNameGlobal(e){return this.all("SELECT * FROM exports WHERE name = ?",e)}findAtLine(e,t){return this.get(`
+      `,e,t)}};var G=class s extends E{static HTTP_METHOD_EXPORTS=new Set(["GET","POST","PUT","PATCH","DELETE","HEAD","OPTIONS"]);findByNameAndFile(e,t){return this.all("SELECT * FROM exports WHERE file_path = ? AND name = ?",t,e)}findByNameGlobal(e){return this.all("SELECT * FROM exports WHERE name = ?",e)}findTopLevelByNameGlobal(e){return this.all("SELECT * FROM exports WHERE name = ? AND parent_id IS NULL",e)}findAtLine(e,t){return this.get(`
       SELECT * FROM exports 
       WHERE file_path = ? AND start_line <= ? AND end_line >= ?
       ORDER BY (end_line - start_line) ASC -- Get innermost symbol
@@ -187,7 +164,7 @@ var at=Object.defineProperty;var P=(s,e)=>()=>(s&&(e=s(s=0)),e);var lt=(s,e)=>{f
       SELECT * FROM exports 
       WHERE lower(name) LIKE ?
       LIMIT ?
-    `,`%${e.toLowerCase()}%`,t)}getAllNames(e=5e3){return this.all("SELECT DISTINCT name FROM exports WHERE parent_id IS NULL LIMIT ?",e).map(i=>i.name)}countByFile(e){return this.get("SELECT COUNT(*) as count FROM exports WHERE file_path = ?",e)?.count||0}findDeadExports(e={}){let{limit:t=50,includeTests:i=!1,includeMigrations:n=!1,includeFixtures:r=!1,excludePatterns:c=[],confidenceThreshold:l="all"}=e,a=[];i||(a.push("e.file_path NOT LIKE '%/test/%'"),a.push("e.file_path NOT LIKE '%/tests/%'"),a.push("e.file_path NOT LIKE '%/__tests__/%'"),a.push("e.file_path NOT LIKE '%.spec.%'"),a.push("e.file_path NOT LIKE '%.test.%'")),n||(a.push("e.file_path NOT LIKE '%/migrations/%'"),a.push("e.file_path NOT LIKE '%/migration/%'"),a.push("e.file_path NOT LIKE '%Migration.%'")),r||(a.push("e.file_path NOT LIKE '%/__fixtures__/%'"),a.push("e.file_path NOT LIKE '%/__mocks__/%'"),a.push("e.file_path NOT LIKE '%/fixtures/%'"),a.push("e.file_path NOT LIKE '%/mocks/%'"),a.push("e.file_path NOT LIKE '%.fixture.%'"),a.push("e.file_path NOT LIKE '%.mock.%'"));for(let g of c){let T=g.replace(/\*\*/g,"%").replace(/\*/g,"%").replace(/\?/g,"_");a.push(`e.file_path NOT LIKE '${T}'`)}let o=a.length>0?`AND ${a.join(" AND ")}`:"",p=this.all(`
+    `,`%${e.toLowerCase()}%`,t)}getAllNames(e=5e3){return this.all("SELECT DISTINCT name FROM exports WHERE parent_id IS NULL LIMIT ?",e).map(i=>i.name)}countByFile(e){return this.get("SELECT COUNT(*) as count FROM exports WHERE file_path = ?",e)?.count||0}findDeadExports(e={}){let{limit:t=50,includeTests:i=!1,includeMigrations:n=!1,includeFixtures:r=!1,excludePatterns:c=[],confidenceThreshold:l="all"}=e,a=[];i||(a.push("e.file_path NOT LIKE '%/test/%'"),a.push("e.file_path NOT LIKE '%/tests/%'"),a.push("e.file_path NOT LIKE '%/__tests__/%'"),a.push("e.file_path NOT LIKE '%.spec.%'"),a.push("e.file_path NOT LIKE '%.test.%'")),n||(a.push("e.file_path NOT LIKE '%/migrations/%'"),a.push("e.file_path NOT LIKE '%/migration/%'"),a.push("e.file_path NOT LIKE '%Migration.%'")),r||(a.push("e.file_path NOT LIKE '%/__fixtures__/%'"),a.push("e.file_path NOT LIKE '%/__mocks__/%'"),a.push("e.file_path NOT LIKE '%/fixtures/%'"),a.push("e.file_path NOT LIKE '%/mocks/%'"),a.push("e.file_path NOT LIKE '%.fixture.%'"),a.push("e.file_path NOT LIKE '%.mock.%'")),a.push("e.file_path NOT LIKE '%/dist/%'"),a.push("e.file_path NOT LIKE '%/build/%'"),a.push("e.file_path NOT LIKE '%/.next/%'"),a.push("e.file_path NOT LIKE '%/.nuxt/%'"),a.push("e.file_path NOT LIKE '%/.cache/%'"),a.push("e.file_path NOT LIKE '%/coverage/%'"),a.push("e.file_path NOT LIKE '%/node_modules/%'"),a.push("e.file_path NOT LIKE '%/storage/runtime/%'"),a.push("e.file_path NOT LIKE '%/compiled_templates/%'"),a.push("e.file_path NOT LIKE '%/compiled_classes/%'"),a.push("e.file_path NOT LIKE '%.generated.%'"),a.push("e.file_path NOT LIKE '%.gen.%'");for(let g of c){let T=g.replace(/\*\*/g,"%").replace(/\*/g,"%").replace(/\?/g,"_");a.push(`e.file_path NOT LIKE '${T}'`)}let o=a.length>0?`AND ${a.join(" AND ")}`:"",p=this.all(`
         SELECT e.name, e.kind, e.file_path, e.start_line
         FROM exports e
         WHERE e.kind IN (
@@ -208,7 +185,7 @@ var at=Object.defineProperty;var P=(s,e)=>()=>(s&&(e=s(s=0)),e);var lt=(s,e)=>{f
         AND NOT EXISTS (SELECT 1 FROM imports i WHERE i.resolved_path = e.file_path AND i.imported_symbols LIKE '%*%')
         ORDER BY e.file_path, e.start_line
         LIMIT ?
-    `,t*2).filter(g=>!this.isFrameworkEntrypointExport(g)).map(g=>{let{confidence:T,reason:N}=this.scoreDeadExportConfidence(g);return{...g,confidence:T,reason:N}}),y=p;return l==="high"?y=p.filter(g=>g.confidence==="high"):l==="medium"&&(y=p.filter(g=>g.confidence==="high"||g.confidence==="medium")),y.slice(0,t)}scoreDeadExportConfidence(e){let t=e.file_path.toLowerCase(),i=e.name;return t.includes("/index.")||t.endsWith("index.ts")||t.endsWith("index.js")?{confidence:"low",reason:"Barrel/index file - likely re-export"}:e.kind==="TsInterfaceDeclaration"||e.kind==="TsTypeAliasDeclaration"?{confidence:"medium",reason:"Type definition - may be used externally"}:t.includes("/entry/")||t.includes("/bin/")||t.includes("main.")||t.includes("server.")||t.includes("cli.")?{confidence:"medium",reason:"Entry point - may be invoked externally"}:(t.includes("/components/")||t.endsWith(".tsx")||t.endsWith(".jsx"))&&/^[A-Z][A-Za-z0-9_]*$/.test(i)?{confidence:"medium",reason:"Component export - may be used by runtime composition"}:(t.includes("/contexts/")||t.includes("/context/"))&&(/Provider$/.test(i)||i.startsWith("use"))?{confidence:"medium",reason:"Context/provider export - may be wired dynamically"}:i.startsWith("create")||i.endsWith("Factory")||i.endsWith("Builder")?{confidence:"medium",reason:"Factory/builder pattern - may be used dynamically"}:i.startsWith("use")&&i.length>3?{confidence:"medium",reason:"Hook pattern - may be used in components"}:{confidence:"high",reason:"No detected usage"}}isFrameworkEntrypointExport(e){let i=e.file_path.toLowerCase().replace(/\\/g,"/"),n=e.name;return!!(/(^|\/)(src\/)?app\/.*\/route\.(t|j)sx?$/.test(i)&&s.HTTP_METHOD_EXPORTS.has(n)||/(^|\/)(src\/)?app\/.*\/(page|layout|loading|error|not-found|default|template)\.(t|j)sx?$/.test(i)||/(^|\/)(src\/)?middleware\.(t|j)sx?$/.test(i)||i.includes("/routes/")&&["loader","action","meta","headers"].includes(n))}getGravityMap(e=[],t){let i={},n=`
+    `,t*2).filter(g=>!this.isFrameworkEntrypointExport(g)).map(g=>{let{confidence:T,reason:N}=this.scoreDeadExportConfidence(g);return{...g,confidence:T,reason:N}}),y=p;return l==="high"?y=p.filter(g=>g.confidence==="high"):l==="medium"&&(y=p.filter(g=>g.confidence==="high"||g.confidence==="medium")),y.slice(0,t)}scoreDeadExportConfidence(e){let t=e.file_path.toLowerCase(),i=e.name;return t.includes("/index.")||t.endsWith("index.ts")||t.endsWith("index.js")?{confidence:"low",reason:"Barrel/index file - likely re-export"}:e.kind==="TsInterfaceDeclaration"||e.kind==="TsTypeAliasDeclaration"?{confidence:"medium",reason:"Type definition - may be used externally"}:t.includes("/entry/")||t.includes("/bin/")||t.includes("main.")||t.includes("server.")||t.includes("cli.")?{confidence:"medium",reason:"Entry point - may be invoked externally"}:(t.includes("/components/")||t.endsWith(".tsx")||t.endsWith(".jsx"))&&/^[A-Z][A-Za-z0-9_]*$/.test(i)?{confidence:"medium",reason:"Component export - may be used by runtime composition"}:(t.includes("/contexts/")||t.includes("/context/"))&&(/Provider$/.test(i)||i.startsWith("use"))?{confidence:"medium",reason:"Context/provider export - may be wired dynamically"}:i.startsWith("create")||i.endsWith("Factory")||i.endsWith("Builder")?{confidence:"medium",reason:"Factory/builder pattern - may be used dynamically"}:i.startsWith("use")&&i.length>3?{confidence:"medium",reason:"Hook pattern - may be used in components"}:{confidence:"high",reason:"No detected usage"}}isFrameworkEntrypointExport(e){let i=e.file_path.toLowerCase().replace(/\\/g,"/"),n=e.name;return!!(/(^|\/)(src\/)?app\/.*\/route\.(t|j)sx?$/.test(i)&&s.HTTP_METHOD_EXPORTS.has(n)||/(^|\/)(src\/)?app\/.*\/(page|layout|loading|error|not-found|default|template)\.(t|j)sx?$/.test(i)||/(^|\/)(src\/)?middleware\.(t|j)sx?$/.test(i)||i.includes("/app/exceptions/handler.php")||i.includes("/app/http/middleware/")||i.includes("/app/providers/")||i.includes("/app/console/commands/")||i.includes("/database/seeds/")||i.includes("/config/")&&i.endsWith(".php")||i.includes("/routes/")&&["loader","action","meta","headers"].includes(n))}getGravityMap(e=[],t){let i={},n=`
       SELECT ws.symbol_id, m.name as mission_name, m.status
       FROM working_set ws
       JOIN missions m ON ws.mission_id = m.id
@@ -263,7 +240,99 @@ var at=Object.defineProperty;var P=(s,e)=>()=>(s&&(e=s(s=0)),e);var lt=(s,e)=>{f
           'inbound' AS direction
         FROM type_graph_edges
         WHERE target_symbol_name = ?
-      `,u=[e];r&&(o+=" AND relationship = ?",u.push(r)),o+=" ORDER BY file_path ASC, line_number ASC, source_symbol_name ASC LIMIT ?",u.push(l),a.push(...this.all(o,...u))}return a.slice(0,l)}findTypeGraphEdgesBySymbolId(e,t={}){let i=this.findById(e);return i?this.findTypeGraphEdges(i.name,{...t,filePath:i.file_path}):[]}};var Ie=`
+      `,u=[e];r&&(o+=" AND relationship = ?",u.push(r)),o+=" ORDER BY file_path ASC, line_number ASC, source_symbol_name ASC LIMIT ?",u.push(l),a.push(...this.all(o,...u))}return a.slice(0,l)}findTypeGraphEdgesBySymbolId(e,t={}){let i=this.findById(e);return i?this.findTypeGraphEdges(i.name,{...t,filePath:i.file_path}):[]}};import Mt from"path";var Nt=new Set(["any","unknown","never","void","null","undefined","string","number","boolean","symbol","object","bigint","readonly","keyof","infer","extends","implements","class","interface","type","function","new"]);function It(s,e){if(!s)return!1;let t=s.trim();return!t||Nt.has(t.toLowerCase())||e.has(t)?!1:/^[A-Za-z_$][A-Za-z0-9_$.]*$/.test(t)}function Ot(s){return s.split(/[,|&]/).map(e=>e.trim()).filter(Boolean)}function Ct(s){let e=s.replace(/^[({[]+/,"").replace(/[)}\]]+$/,"").replace(/^readonly\s+/,"").trim();return e&&e.match(/^([A-Za-z_$][A-Za-z0-9_$.]*)/)?.[1]||null}function At(s){let e=[],t=0,i="",n=!1;for(let r of s){if(r==="<"&&(t++,t===1)){n=!0,i="";continue}if(r===">"&&(t>0&&t--,t===0&&n)){n=!1,i.trim()&&e.push(i),i="";continue}n&&(i+=r)}return e}function Dt(s){let e=new Set;for(let t of s){let i=t.split(",").map(n=>n.trim());for(let n of i){let r=n.match(/^([A-Za-z_$][A-Za-z0-9_$]*)/);r?.[1]&&e.add(r[1])}}return e}function ae(s,e){let t=[];for(let i of Ot(s)){let n=Ct(i);n&&It(n,e)&&t.push(n)}return t}function Ie(s){if(!s)return[];let e=s.replace(/\s+/g," ").trim();if(!e)return[];let t=At(e),i=Dt(t),n=[],r=new Set,c=(o,u,m)=>{let p=`${o}:${u}`;r.has(p)||(r.add(p),n.push({relationship:o,targetName:u,...m?{metadata:m}:{}}))},l=e.match(/\bextends\s+(.+?)(?=\bimplements\b|\{|=|$)/);if(l?.[1]){let o=ae(l[1],i);for(let u of o)c("extends",u,l[1].trim())}let a=e.match(/\bimplements\s+(.+?)(?=\{|=|$)/);if(a?.[1]){let o=ae(a[1],i);for(let u of o)c("implements",u,a[1].trim())}for(let o of t){let u=/([A-Za-z_$][A-Za-z0-9_$]*)\s+extends\s+([^,>]+)/g,m=null;for(;(m=u.exec(o))!==null;){let p=m[2]?.trim();if(!p)continue;let y=ae(p,i);for(let g of y)c("constrained_by",g,p)}}return n}var V=class extends E{findByPath(e){return this.get("SELECT * FROM files WHERE path = ?",e)}findAll(e){let t="SELECT * FROM files ORDER BY path ASC";return e&&(t+=` LIMIT ${e}`),this.all(t)}getAllPaths(){return this.all("SELECT path FROM files").map(t=>t.path)}findInSubPath(e,t){let i=Mt.resolve(e,t),n=i.endsWith("/")?i:i+"/";return this.all(`
+      SELECT * FROM files 
+      WHERE (path LIKE ? OR path = ?)
+      ORDER BY path ASC
+    `,`${n}%`,i)}findWithEmbeddings(){return this.all("SELECT * FROM files WHERE embedding IS NOT NULL")}findFts(e,t=10){return this.all(`
+      SELECT files.*, files_fts.rank
+      FROM files_fts
+      JOIN files ON files.rowid = files_fts.rowid
+      WHERE files_fts MATCH ?
+      ORDER BY rank
+      LIMIT ?
+    `,e,t)}findByPathKeywords(e,t=10){let i=e.map(()=>"LOWER(path) LIKE ?").join(" OR ");return this.all(`
+      SELECT * FROM files 
+      WHERE ${i}
+      LIMIT ?
+    `,...e.map(n=>`%${n}%`),t)}findContentFts(e,t=50){let i=this.buildContentFtsQuery(e);return i?this.all(`
+      SELECT
+        files.*,
+        bm25(content_fts, 0.2, 1.0) AS bm25_rank
+      FROM content_fts
+      JOIN files ON files.path = content_fts.file_path
+      WHERE content_fts MATCH ?
+      ORDER BY bm25_rank ASC
+      LIMIT ?
+    `,i,Math.max(1,Math.min(t,1e3))):[]}getContent(e){return this.get("SELECT content FROM file_content WHERE file_path = ?",e)?.content}findContentByToken(e,t=10){return this.all(`
+          SELECT file_path 
+          FROM content_fts 
+          WHERE content_fts MATCH ? 
+            AND (file_path LIKE '%.ts' OR file_path LIKE '%.tsx' OR file_path LIKE '%.js' OR file_path LIKE '%.py' OR file_path LIKE '%.php')
+            AND file_path NOT LIKE '%/test/%'
+            AND file_path NOT LIKE '%.spec.%'
+          LIMIT ?
+        `,`"${e.replace(/[^a-zA-Z0-9_/]/g," ")}"`,t).map(n=>n.file_path)}findSynapses(e){let t="SELECT * FROM event_synapses WHERE 1=1",i=[];if(e.type&&(t+=" AND type = ?",i.push(e.type)),e.name){let n=e.name;n.startsWith("/")&&(n=n.substring(1)),n.endsWith("/")&&(n=n.substring(0,n.length-1)),n.length>0&&(t+=" AND (name LIKE ? OR name LIKE ? OR name = ?)",i.push(`${n}%`),i.push(`%/${n}%`),i.push(e.name))}return e.direction&&(t+=" AND direction = ?",i.push(e.direction)),t+=` LIMIT ${e.limit||50}`,this.all(t,...i)}exists(e){return!!this.get("SELECT 1 FROM files WHERE path = ?",e)}update(e,t){let i=Object.keys(t);if(i.length===0)return;let n=i.map(c=>`${c} = ?`).join(", "),r=Object.values(t);r.push(e),this.run(`UPDATE files SET ${n} WHERE path = ?`,...r)}getStats(){let e=this.get(`
+      SELECT
+        COUNT(*) as total,
+        SUM(CASE WHEN summary IS NOT NULL AND summary != '' THEN 1 ELSE 0 END) as withSummary
+      FROM files
+    `);return{total:e?.total||0,withSummary:e?.withSummary||0}}getGravityMap(e=[],t){let i={},n=`
+      SELECT ws.file_path, m.name as mission_name, m.status
+      FROM working_set ws
+      JOIN missions m ON ws.mission_id = m.id
+      WHERE (
+        (m.status IN ('in-progress', 'verifying') ${t?"AND m.git_branch = ?":""})
+        OR m.id IN (${e.length>0?e.join(","):"-1"})
+      )
+      AND ws.file_path IS NOT NULL
+    `,r=[];t&&r.push(t);let c=this.all(n,...r);for(let o of c){i[o.file_path]||(i[o.file_path]={score:1,reasons:[]});let u=o.status==="in-progress"||o.status==="verifying"?1:.5;i[o.file_path].score+=u;let m=o.status==="in-progress"||o.status==="verifying"?"Working Set":"Lineage Bleed";i[o.file_path].reasons.push(`${m}: ${o.mission_name}`)}let l=Math.floor(Date.now()/1e3)-86400,a=this.all(`
+      SELECT file_path, type, mission_id
+      FROM intent_logs
+      WHERE (created_at > ? OR mission_id IN (${e.length>0?e.join(","):"-1"}))
+      AND file_path IS NOT NULL
+      ORDER BY created_at DESC
+      LIMIT 100
+    `,l);for(let o of a){i[o.file_path]||(i[o.file_path]={score:1,reasons:[]});let u=o.mission_id?e.includes(o.mission_id):!1,m=u?.1:.2;i[o.file_path].score<5&&(i[o.file_path].score+=m);let p=u?`Lineage Intent: ${o.type}`:`Recent Intent: ${o.type}`;!i[o.file_path].reasons.includes(p)&&i[o.file_path].reasons.length<5&&i[o.file_path].reasons.push(p)}return i}getCount(){return this.get("SELECT COUNT(*) as count FROM files")?.count||0}getTopDirectories(e,t=8){return this.all(`
+        SELECT 
+            SUBSTR(path, LENGTH(?) + 2, 
+                INSTR(SUBSTR(path, LENGTH(?) + 2), '/') - 1
+            ) as root,
+            COUNT(*) as total_files,
+            SUM(CASE 
+                WHEN path LIKE '%.ts' OR path LIKE '%.tsx' 
+                  OR path LIKE '%.js' OR path LIKE '%.jsx' 
+                  OR path LIKE '%.mjs' OR path LIKE '%.cjs' 
+                THEN 1 ELSE 0 
+            END) as ts_files
+        FROM files 
+        WHERE path LIKE ? || '/%/%'
+        GROUP BY root
+        ORDER BY total_files DESC
+        LIMIT ?
+    `,e,e,e,t)}hasFilesPattern(e){return!!this.get("SELECT 1 FROM files WHERE path LIKE ? LIMIT 1",e)}findPackageJsonChildren(e){return this.all(`
+        SELECT
+            path,
+            SUBSTR(path, LENGTH(?) + 2) as relPath
+        FROM files
+        WHERE path LIKE ? || '/%/package.json'
+    `,e,e)}deletePaths(e){if(e.length===0)return;let t=this.db.prepare("DELETE FROM files WHERE path = ?");this.db.transaction(n=>{for(let r of n)t.run(r)})(e)}updateMtime(e,t){this.run("UPDATE files SET mtime = ? WHERE path = ?",t,e)}batchSaveIndexResults(e,t,i,n){let r=this.db.prepare("DELETE FROM exports WHERE file_path = ?"),c=this.db.prepare("DELETE FROM imports WHERE file_path = ?"),l=this.db.prepare("DELETE FROM configs WHERE file_path = ?"),a=this.db.prepare("DELETE FROM file_content WHERE file_path = ?"),o=this.db.prepare("DELETE FROM event_synapses WHERE file_path = ?"),u=this.db.prepare("DELETE FROM type_graph_edges WHERE file_path = ?"),m=this.db.prepare("INSERT INTO exports (file_path, name, kind, signature, doc, start_line, end_line, classification, capabilities, parent_id, embedding) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)"),p=this.db.prepare("INSERT INTO imports (file_path, module_specifier, imported_symbols, resolved_path) VALUES (?, ?, ?, ?)"),y=this.db.prepare("INSERT INTO configs (file_path, key, value, kind) VALUES (?, ?, ?, ?)"),g=this.db.prepare("INSERT INTO file_content (file_path, content) VALUES (?, ?)"),T=this.db.prepare("INSERT INTO event_synapses (file_path, type, name, direction, line_number, code_snippet) VALUES (?, ?, ?, ?, ?, ?)"),N=this.db.prepare("INSERT INTO type_graph_edges (file_path, source_symbol_id, source_symbol_name, target_symbol_name, relationship, line_number, metadata) VALUES (?, ?, ?, ?, ?, ?, ?)"),Je=this.db.prepare(`
+        INSERT INTO files (path, mtime, last_scanned_at, classification, summary, embedding, content_hash)
+        VALUES (?, ?, ?, ?, ?, ?, ?)
+        ON CONFLICT(path) DO UPDATE SET
+            mtime=excluded.mtime,
+            last_scanned_at=excluded.last_scanned_at,
+            classification=excluded.classification,
+            summary=excluded.summary,
+            embedding=excluded.embedding,
+            content_hash=excluded.content_hash
+    `),Qe=this.db.transaction(C=>{for(let Xe of C){let{meta:_,exports:Ee,imports:he,configs:fe,events:ge,content:U,classification:Ze,summary:et,embedding:_e,contentHash:tt}=Xe;r.run(_.path),c.run(_.path),l.run(_.path),a.run(_.path),o.run(_.path),u.run(_.path);let it=tt??(U&&i?i(U):null);if(Je.run(_.path,_.mtime,Date.now(),Ze||"Unknown",et||"",_e?JSON.stringify(_e):null,it),Ee){let h=(w,nt,st)=>{for(let f of nt){let rt=f.embedding?JSON.stringify(f.embedding):null,be=m.run(w,f.name,f.kind,f.signature,f.doc||"",f.line,f.endLine||f.line,f.classification||"Other",f.capabilities||"[]",st,rt),ye=Number(be.lastInsertRowid);if(Number.isFinite(ye)){let ot=Ie(f.signature);for(let B of ot)B.targetName!==f.name&&N.run(w,ye,f.name,B.targetName,B.relationship,f.line,B.metadata||null)}f.members&&f.members.length>0&&h(w,f.members,be.lastInsertRowid)}};h(_.path,Ee,null)}if(he)for(let h of he){let w=h.resolved_path!==void 0?h.resolved_path:n?.(h.module,_.path,t)??"";p.run(_.path,h.module,h.name,w)}if(fe)for(let h of fe)y.run(_.path,h.key,h.value,h.kind);if(U!==void 0&&g.run(_.path,U),ge)for(let h of ge)T.run(_.path,h.type,h.name,h.direction,h.line,h.snippet)}}),pe=500;for(let C=0;C<e.length;C+=pe)Qe(e.slice(C,C+pe))}getLatestScanTime(){return this.get("SELECT MAX(last_scanned_at) as t FROM files")?.t||null}buildContentFtsQuery(e){let t=e.replace(/([a-z0-9])([A-Z])/g,"$1 $2").toLowerCase().split(/[^a-z0-9_]+/).map(r=>r.trim()).filter(r=>r.length>=2).slice(0,12);if(t.length===0)return"";if(t.length===1)return`${t[0]}*`;let i=`"${t.join(" ")}"`,n=t.map(r=>`${r}*`).join(" OR ");return`${i} OR ${n}`}};var J=class extends E{getSection(e){return this.get("SELECT section, data, updated_at FROM hologram_snapshot WHERE section = ?",e)}getAllSections(){return this.all("SELECT section, data, updated_at FROM hologram_snapshot ORDER BY section")}upsertSection(e,t){this.run(`
+      INSERT INTO hologram_snapshot (section, data, updated_at)
+      VALUES (?, ?, unixepoch())
+      ON CONFLICT(section) DO UPDATE SET
+        data = excluded.data,
+        updated_at = excluded.updated_at
+    `,e,t)}deleteSection(e){this.run("DELETE FROM hologram_snapshot WHERE section = ?",e)}deleteAll(){this.run("DELETE FROM hologram_snapshot")}hasSection(e){return(this.get("SELECT COUNT(*) as count FROM hologram_snapshot WHERE section = ?",e)?.count??0)>0}};var Oe=`
 WITH RECURSIVE dependency_chain AS (
     -- Base case: Direct dependents of the target symbol
     -- Meaning: Files that import the file where the symbol is defined
@@ -314,7 +383,7 @@ SELECT DISTINCT
     dc.imported_symbols
 FROM dependency_chain dc
 ORDER BY dc.depth, dc.consumer_path;
-`;var q=class extends E{findByFile(e){return this.all("SELECT * FROM imports WHERE file_path = ?",e)}findByFiles(e){if(e.length===0)return[];let t=e.map(()=>"?").join(", ");return this.all(`SELECT * FROM imports WHERE file_path IN (${t}) ORDER BY file_path`,...e)}getAllResolved(){return this.all(`
+`;var Q=class extends E{findByFile(e){return this.all("SELECT * FROM imports WHERE file_path = ?",e)}findByFiles(e){if(e.length===0)return[];let t=e.map(()=>"?").join(", ");return this.all(`SELECT * FROM imports WHERE file_path IN (${t}) ORDER BY file_path`,...e)}getAllResolved(){return this.all(`
             SELECT * FROM imports 
             WHERE resolved_path IS NOT NULL AND resolved_path != ''
         `)}findDependents(e){return this.all("SELECT * FROM imports WHERE resolved_path = ?",e)}countByFile(e){return this.get("SELECT COUNT(*) as count FROM imports WHERE file_path = ?",e)?.count||0}countDependents(e){return this.get("SELECT COUNT(*) as count FROM imports WHERE resolved_path = ?",e)?.count||0}getImportsForFile(e){return this.all("SELECT module_specifier, imported_symbols, resolved_path FROM imports WHERE file_path = ?",e)}findImportSource(e,t){return this.get(`
@@ -340,7 +409,116 @@ ORDER BY dc.depth, dc.consumer_path;
             SELECT COUNT(*) as count FROM imports 
             WHERE resolved_path IN (${i})
             AND (imported_symbols LIKE ? OR imported_symbols = '' OR imported_symbols = '*')
-        `,...e,`%${t}%`)?.count||0}findImpactDependents(e,t,i){return this.all(Ie,e,t,i,t)}getCount(){return this.get("SELECT COUNT(*) as count FROM imports")?.count||0}};var V=class extends E{findById(e){return this.get("SELECT * FROM missions WHERE id = ?",e)}findByIds(e){if(e.length===0)return[];let t=e.map(()=>"?").join(", ");return this.all(`SELECT * FROM missions WHERE id IN (${t})`,...e)}findActive(e){let t="SELECT * FROM missions WHERE status IN ('in-progress', 'planned', 'verifying')",i=[];return e&&(t+=" AND git_branch = ?",i.push(e)),t+=` ORDER BY 
+        `,...e,`%${t}%`)?.count||0}findImpactDependents(e,t,i){return this.all(Oe,e,t,i,t)}getCount(){return this.get("SELECT COUNT(*) as count FROM imports")?.count||0}};A();var Z=class s extends E{findByMission(e,t=50){return this.all(`
+      SELECT 
+        id, mission_id, symbol_id, file_path, type, content, confidence, 
+        symbol_name, signature, commit_sha, is_crystallized, crystal_id, 
+        created_at
+      FROM intent_logs 
+      WHERE mission_id = ? 
+      ORDER BY created_at DESC 
+      LIMIT ?
+    `,e,t)}findRecentDecisionActivity(e=10){return this.all(`
+      SELECT 
+        id, mission_id, symbol_id, file_path, type, content, confidence, 
+        symbol_name, signature, commit_sha, is_crystallized, crystal_id, 
+        created_at
+      FROM intent_logs 
+      WHERE type IN ('decision', 'system', 'fix', 'heritage', 'adr')
+      ORDER BY created_at DESC 
+      LIMIT ?
+    `,e)}create(e){let t=this.insert(`
+      INSERT INTO intent_logs (mission_id, symbol_id, file_path, type, content, confidence, symbol_name, signature, commit_sha)
+      VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?)
+    `,e.mission_id,e.symbol_id,e.file_path,e.type,e.content,e.confidence,e.symbol_name,e.signature,e.commit_sha);return s.EMBEDDABLE_TYPES.has(e.type)&&this.generateAndStoreEmbedding(Number(t),e).catch(i=>{d.debug({err:i,intentLogId:t},"Failed to generate intent log embedding")}),t}static EMBEDDABLE_TYPES=new Set(["decision","discovery","fix","blocker","note","heritage","crystal"]);static buildEmbeddingText(e){let t=[`[${e.type}]`];return e.symbol_name&&t.push(`symbol: ${e.symbol_name}`),e.file_path&&t.push(`file: ${e.file_path.split("/").pop()}`),t.push(e.content),t.join(" ")}async generateAndStoreEmbedding(e,t){let{generateEmbedding:i}=await Promise.resolve().then(()=>(S(),O)),n=s.buildEmbeddingText(t),r=await i(n);r&&this.run("UPDATE intent_logs SET embedding = ? WHERE id = ?",JSON.stringify(r),e)}findWithEmbeddings(){return this.all("SELECT * FROM intent_logs WHERE embedding IS NOT NULL AND type NOT IN ('system', 'lapsed')")}async findSemanticMatches(e,t,i){let{cosineSimilarity:n}=await Promise.resolve().then(()=>(S(),O)),r=this.findWithEmbeddings();if(r.length>5e3)return d.warn({count:r.length},"Intent log count exceeds brute-force vector scan limit (5000). Skipping semantic recall."),[];let c=[];for(let l of r)if(!(i&&l.symbol_id===i))try{let a=JSON.parse(l.embedding),o=n(e,a);o>.25&&c.push({id:l.id,mission_id:l.mission_id,type:l.type,content:l.content,symbol_name:l.symbol_name,file_path:l.file_path,similarity:o,created_at:l.created_at})}catch{}return c.sort((l,a)=>a.similarity-l.similarity).slice(0,t)}delete(e){this.run("DELETE FROM intent_logs WHERE id = ?",e)}update(e,t){let i=Object.keys(t);if(i.length===0)return;let n=i.map(c=>`${c} = ?`).join(", "),r=Object.values(t);r.push(e),this.run(`UPDATE intent_logs SET ${n} WHERE id = ?`,...r)}findRepairableOrphans(){return this.all(`
+      SELECT id, file_path, symbol_name, signature 
+      FROM intent_logs 
+      WHERE symbol_id IS NULL AND symbol_name IS NOT NULL
+    `)}findOrphans(){return this.all(`
+      SELECT il.id, il.symbol_id, il.file_path, il.symbol_name
+      FROM intent_logs il
+      WHERE (il.symbol_id IS NOT NULL AND NOT EXISTS (SELECT 1 FROM exports e WHERE e.id = il.symbol_id))
+         OR (il.symbol_id IS NULL AND il.type != 'lapsed' AND il.type != 'system' AND il.type != 'adr')
+    `)}findLogsForMissingFiles(){return this.all(`
+      SELECT il.id
+      FROM intent_logs il
+      WHERE il.file_path IS NOT NULL
+      AND NOT EXISTS (
+        SELECT 1 FROM files f WHERE f.path = il.file_path
+      )
+    `)}markAsLapsed(e){this.run(`
+      UPDATE intent_logs 
+      SET symbol_id = NULL, 
+          type = 'lapsed',
+          content = 'Lapsed: ' || content
+      WHERE id = ?
+    `,e)}importHeritage(e,t,i,n){this.run(`
+      INSERT INTO intent_logs (type, content, commit_sha, created_at, confidence, mission_id)
+      VALUES ('heritage', ?, ?, ?, ?, NULL)
+    `,e,t,i,n)}countByType(e){return this.get("SELECT COUNT(*) as count FROM intent_logs WHERE type = ?",e)?.count||0}findRawByMission(e){return this.all(`SELECT 
+        id, mission_id, symbol_id, file_path, type, content, confidence, 
+        symbol_name, signature, commit_sha, is_crystallized, crystal_id, 
+        created_at
+       FROM intent_logs
+       WHERE mission_id = ? AND is_crystallized = 0
+         AND type NOT IN ('adr', 'system', 'crystal', 'lapsed')
+       ORDER BY created_at ASC`,e)}findCrystallizableByMission(e){return this.all(`SELECT
+        id, mission_id, symbol_id, file_path, type, content, confidence,
+        symbol_name, signature, commit_sha, is_crystallized, crystal_id,
+        created_at
+       FROM intent_logs
+       WHERE mission_id = ?
+         AND type NOT IN ('adr', 'system', 'crystal', 'lapsed')
+       ORDER BY created_at ASC`,e)}findCrystalByMission(e){return this.get(`SELECT 
+        id, mission_id, symbol_id, file_path, type, content, confidence, 
+        symbol_name, signature, commit_sha, is_crystallized, crystal_id, 
+        created_at
+       FROM intent_logs
+       WHERE mission_id = ? AND type = 'crystal'
+       ORDER BY created_at DESC LIMIT 1`,e)}findCrystalBySymbol(e){return this.get(`SELECT
+        id, mission_id, symbol_id, file_path, type, content, confidence,
+        symbol_name, signature, commit_sha, is_crystallized, crystal_id,
+        created_at
+       FROM intent_logs
+       WHERE symbol_id = ? AND mission_id IS NULL AND type = 'crystal'
+       ORDER BY created_at DESC LIMIT 1`,e)}crystallize(e,t,i){return this.transaction(()=>{let n=i;return typeof n=="number"?this.run(`UPDATE intent_logs
+           SET content = ?, confidence = 1.0
+           WHERE id = ? AND mission_id = ? AND type = 'crystal'`,t,n,e):n=Number(this.insert(`INSERT INTO intent_logs (mission_id, type, content, confidence, is_crystallized, symbol_id, file_path, symbol_name, signature, commit_sha)
+             VALUES (?, 'crystal', ?, 1.0, 0, NULL, NULL, NULL, NULL, NULL)`,e,t)),this.run(`UPDATE intent_logs
+         SET is_crystallized = 1, crystal_id = ?
+         WHERE mission_id = ? AND is_crystallized = 0 AND id != ?
+           AND type NOT IN ('adr', 'system', 'crystal', 'lapsed')`,n,e,n),this.generateAndStoreEmbedding(n,{type:"crystal",content:t}).catch(r=>{d.debug({err:r,intentLogId:n},"Failed to refresh crystal embedding")}),n})}findRawBySymbol(e){return this.all(`SELECT * FROM intent_logs
+       WHERE symbol_id = ? AND mission_id IS NULL AND is_crystallized = 0
+         AND type NOT IN ('adr', 'system', 'crystal', 'lapsed')
+       ORDER BY created_at ASC`,e)}findCrystallizableBySymbol(e){return this.all(`SELECT
+        id, mission_id, symbol_id, file_path, type, content, confidence,
+        symbol_name, signature, commit_sha, is_crystallized, crystal_id,
+        created_at
+       FROM intent_logs
+       WHERE symbol_id = ? AND mission_id IS NULL
+         AND type NOT IN ('adr', 'system', 'crystal', 'lapsed')
+       ORDER BY created_at ASC`,e)}crystallizeBySymbol(e,t,i){return this.transaction(()=>{let n=i;return typeof n=="number"?this.run(`UPDATE intent_logs
+           SET content = ?, confidence = 1.0
+           WHERE id = ? AND symbol_id = ? AND mission_id IS NULL AND type = 'crystal'`,t,n,e):n=Number(this.insert(`INSERT INTO intent_logs (mission_id, symbol_id, type, content, confidence, is_crystallized, file_path, symbol_name, signature, commit_sha)
+             VALUES (NULL, ?, 'crystal', ?, 1.0, 0, NULL, NULL, NULL, NULL)`,e,t)),this.run(`UPDATE intent_logs
+         SET is_crystallized = 1, crystal_id = ?
+         WHERE symbol_id = ? AND mission_id IS NULL AND is_crystallized = 0 AND id != ?
+           AND type NOT IN ('adr', 'system', 'crystal', 'lapsed')`,n,e,n),this.generateAndStoreEmbedding(n,{type:"crystal",content:t}).catch(r=>{d.debug({err:r,intentLogId:n},"Failed to refresh crystal embedding")}),n})}countByMissions(e){if(e.length===0)return{};let t=e.map(()=>"?").join(","),i=this.all(`SELECT mission_id, COUNT(*) as cnt
+       FROM intent_logs
+       WHERE mission_id IN (${t})
+         AND type NOT IN ('system', 'adr', 'lapsed')
+       GROUP BY mission_id`,...e),n={};for(let r of i)n[r.mission_id]=r.cnt;return n}findMissionsWithBlockers(e){if(e.length===0)return new Set;let t=e.map(()=>"?").join(","),i=this.all(`SELECT DISTINCT mission_id
+       FROM intent_logs
+       WHERE mission_id IN (${t})
+         AND type = 'blocker'`,...e);return new Set(i.map(n=>n.mission_id))}findByMissionPreferCrystal(e,t=50){let i=this.findCrystalByMission(e);if(i){let n=this.all(`SELECT 
+        id, mission_id, symbol_id, file_path, type, content, confidence, 
+        symbol_name, signature, commit_sha, is_crystallized, crystal_id, 
+        created_at
+         FROM intent_logs
+         WHERE mission_id = ? AND is_crystallized = 0 AND type NOT IN ('adr', 'system', 'crystal', 'lapsed')
+           AND created_at > ?
+         ORDER BY created_at DESC LIMIT ?`,e,i.created_at,t-1);return[i,...n]}return this.findByMission(e,t)}async findSemanticTheme(e,t,i=200){let{cosineSimilarity:n}=await Promise.resolve().then(()=>(S(),O)),r=this.findWithEmbeddings(),c=[];for(let l of r)if(s.EMBEDDABLE_TYPES.has(l.type)&&l.type!=="crystal"&&l.mission_id!=null&&!(t&&!t.includes(l.mission_id)))try{let a=JSON.parse(l.embedding),o=n(e,a);o>.35&&c.push({...l,_similarity:o})}catch{}return c.sort((l,a)=>a._similarity-l._similarity).slice(0,i).map(({_similarity:l,...a})=>a)}crystallizeTheme(e,t,i){return this.transaction(()=>{let n=this.insert(`INSERT INTO intent_logs (mission_id, type, content, confidence, is_crystallized, symbol_id, file_path, symbol_name, signature, commit_sha)
+         VALUES (NULL, 'crystal', ?, 1.0, 0, NULL, NULL, NULL, NULL, NULL)`,i);if(t.length>0){let r=t.map(()=>"?").join(",");this.run(`UPDATE intent_logs SET is_crystallized = 1, crystal_id = ? WHERE id IN (${r})`,n,...t)}return n})}async backfillEmbeddings(e=64,t){let{generateEmbeddingsBatch:i}=await Promise.resolve().then(()=>(S(),O)),n=[...s.EMBEDDABLE_TYPES].map(u=>`'${u}'`).join(","),r=this.all(`SELECT * FROM intent_logs WHERE embedding IS NULL AND type IN (${n})`);if(r.length===0)return 0;let c=r.map(u=>s.buildEmbeddingText(u)),l=await i(c,e,t),a=this.db.prepare("UPDATE intent_logs SET embedding = ? WHERE id = ?"),o=0;return this.transaction(()=>{for(let u=0;u<r.length;u++)l[u]&&(a.run(JSON.stringify(l[u]),r[u].id),o++)}),d.info({total:r.length,embedded:o},"Intent log embedding backfill complete"),o}};var ee=class extends E{findById(e){return this.get("SELECT * FROM missions WHERE id = ?",e)}findByIds(e){if(e.length===0)return[];let t=e.map(()=>"?").join(", ");return this.all(`SELECT * FROM missions WHERE id IN (${t})`,...e)}findActive(e){let t="SELECT * FROM missions WHERE status IN ('in-progress', 'planned', 'verifying')",i=[];return e&&(t+=" AND git_branch = ?",i.push(e)),t+=` ORDER BY 
         CASE WHEN status = 'in-progress' THEN 0 WHEN status = 'verifying' THEN 1 ELSE 2 END, 
         created_at ASC`,this.all(t,...i)}findAll(e){let t="SELECT * FROM missions",i=[];return e&&(t+=" WHERE status = ?",i.push(e)),t+=` ORDER BY 
         CASE WHEN status = 'in-progress' THEN 0 WHEN status = 'verifying' THEN 1 ELSE 2 END, 
@@ -412,7 +590,43 @@ ORDER BY dc.depth, dc.consumer_path;
        SET status = 'in-progress', updated_at = unixepoch() 
        WHERE git_branch = ? AND status = 'suspended'`,e)}findMergedMissions(e,t){if(t.length===0)return[];let i=t.filter(r=>r!==e);if(i.length===0)return[];let n=i.map(()=>"?").join(",");return this.all(`SELECT * FROM missions 
        WHERE status IN ('in-progress', 'planned', 'verifying', 'suspended')
-       AND git_branch IN (${n})`,...i)}findByCommitShas(e){if(e.length===0)return[];let t=e.map(()=>"?").join(",");return this.all(`SELECT * FROM missions WHERE commit_sha IN (${t})`,...e)}findByParentId(e){return this.all("SELECT * FROM missions WHERE parent_id = ?",e)}hasChildren(e){return!!this.get("SELECT 1 FROM missions WHERE parent_id = ? LIMIT 1",e)}hasNoSteps(e){if(!e.strategy_graph)return!0;try{let t=JSON.parse(e.strategy_graph),i=t?.steps??t;return!Array.isArray(i)||i.length===0}catch{return!0}}findParentOnlyIds(e){return e.filter(t=>t.parent_id!=null||!this.hasChildren(t.id)?!1:this.hasNoSteps(t)).map(t=>t.id)}createLink(e,t,i,n,r){this.db.exec(`
+       AND git_branch IN (${n})`,...i)}findByCommitShas(e){if(e.length===0)return[];let t=e.map(()=>"?").join(",");return this.all(`SELECT * FROM missions WHERE commit_sha IN (${t})`,...e)}findByParentId(e){return this.all("SELECT * FROM missions WHERE parent_id = ?",e)}hasChildren(e){return!!this.get("SELECT 1 FROM missions WHERE parent_id = ? LIMIT 1",e)}hasNoSteps(e){if(!e.strategy_graph)return!0;try{let t=JSON.parse(e.strategy_graph),i=t?.steps??t;return!Array.isArray(i)||i.length===0}catch{return!0}}findParentOnlyIds(e){return e.filter(t=>t.parent_id!=null||!this.hasChildren(t.id)?!1:this.hasNoSteps(t)).map(t=>t.id)}createLink(e,t,i,n,r){return this.ensureCrossRepoLinksSchema(),this.run(`
+      INSERT OR IGNORE INTO cross_repo_links (mission_id, linked_repo_path, linked_mission_id, relationship, direction)
+      VALUES (?, ?, ?, ?, ?)
+    `,e,t,i,n,r)}getLink(e,t,i,n){return this.ensureCrossRepoLinksSchema(),this.get(`
+      SELECT relationship, direction
+      FROM cross_repo_links
+      WHERE mission_id = ?
+        AND linked_repo_path = ?
+        AND linked_mission_id = ?
+        AND direction = ?
+      LIMIT 1
+    `,e,t,i,n)}upsertLink(e,t,i,n,r){return this.ensureCrossRepoLinksSchema(),this.run(`
+      INSERT INTO cross_repo_links (
+        mission_id,
+        linked_repo_path,
+        linked_mission_id,
+        relationship,
+        direction
+      )
+      VALUES (?, ?, ?, ?, ?)
+      ON CONFLICT(mission_id, linked_repo_path, linked_mission_id, direction)
+      DO UPDATE SET relationship = excluded.relationship
+    `,e,t,i,n,r)}hasLink(e,t,i,n){return this.ensureCrossRepoLinksSchema(),!!this.get(`
+      SELECT id
+      FROM cross_repo_links
+      WHERE mission_id = ?
+        AND linked_repo_path = ?
+        AND linked_mission_id = ?
+        AND direction = ?
+      LIMIT 1
+    `,e,t,i,n)}deleteLink(e,t,i,n){return this.ensureCrossRepoLinksSchema(),this.run(`
+      DELETE FROM cross_repo_links
+      WHERE mission_id = ?
+        AND linked_repo_path = ?
+        AND linked_mission_id = ?
+        AND direction = ?
+    `,e,t,i,n)}ensureCrossRepoLinksSchema(){this.db.exec(`
             CREATE TABLE IF NOT EXISTS cross_repo_links (
                 id INTEGER PRIMARY KEY AUTOINCREMENT,
                 mission_id INTEGER NOT NULL,
@@ -424,175 +638,20 @@ ORDER BY dc.depth, dc.consumer_path;
                 FOREIGN KEY(mission_id) REFERENCES missions(id) ON DELETE CASCADE
             );
             CREATE INDEX IF NOT EXISTS idx_cross_repo_mission ON cross_repo_links(mission_id);
-    `),this.run(`
-      INSERT INTO cross_repo_links (mission_id, linked_repo_path, linked_mission_id, relationship, direction)
-      VALUES (?, ?, ?, ?, ?)
-    `,e,t,i,n,r)}getLinks(e){try{return this.all(`
+            CREATE UNIQUE INDEX IF NOT EXISTS idx_cross_repo_unique
+              ON cross_repo_links(mission_id, linked_repo_path, linked_mission_id, direction);
+    `)}getLinks(e){try{return this.all(`
         SELECT linked_repo_path, linked_mission_id, relationship, direction
         FROM cross_repo_links
         WHERE mission_id = ?
-      `,e)}catch{return[]}}findLastMission(){return this.get("SELECT * FROM missions ORDER BY updated_at DESC, id DESC LIMIT 1")}findActiveByPriority(){return this.get("SELECT * FROM missions WHERE status IN ('in-progress', 'active', 'verifying') ORDER BY CASE WHEN status = 'in-progress' THEN 0 ELSE 1 END, created_at ASC LIMIT 1")}addHandoff(e,t){let i=JSON.stringify(t),n=e??0,r=this.insert("INSERT INTO mission_artifacts (mission_id, type, identifier, metadata) VALUES (?, ?, ?, ?)",n,"handoff",t.kind,i),c=[`[handoff:${t.kind}]`,...t.findings.map(l=>l.statement),...t.risks.map(l=>l.description),...t.gaps].filter(Boolean).join(" ");return Promise.resolve().then(()=>(L(),I)).then(({generateEmbedding:l})=>l(c)).then(l=>{l&&this.run("UPDATE mission_artifacts SET embedding = ? WHERE id = ?",JSON.stringify(l),r)}).catch(()=>{}),r}getHandoffs(e,t,i=20){let n=["type = 'handoff'"],r=[];e!==void 0&&(n.push("mission_id = ?"),r.push(e??0)),t&&(n.push("identifier = ?"),r.push(t));let c=`SELECT * FROM mission_artifacts WHERE ${n.join(" AND ")} ORDER BY created_at DESC LIMIT ?`;return r.push(i),this.all(c,...r)}async findSemanticHandoffs(e,t=5){let{cosineSimilarity:i}=await Promise.resolve().then(()=>(L(),I)),n=this.all("SELECT * FROM mission_artifacts WHERE type = 'handoff' AND embedding IS NOT NULL"),r=[];for(let c of n)try{let l=JSON.parse(c.embedding),a=i(e,l);a>.3&&r.push({...c,similarity:a})}catch{}return r.sort((c,l)=>l.similarity-c.similarity).slice(0,t)}};M();var J=class s extends E{findByMission(e,t=50){return this.all(`
-      SELECT 
-        id, mission_id, symbol_id, file_path, type, content, confidence, 
-        symbol_name, signature, commit_sha, is_crystallized, crystal_id, 
-        created_at
-      FROM intent_logs 
-      WHERE mission_id = ? 
-      ORDER BY created_at DESC 
-      LIMIT ?
-    `,e,t)}findRecentDecisionActivity(e=10){return this.all(`
-      SELECT 
-        id, mission_id, symbol_id, file_path, type, content, confidence, 
-        symbol_name, signature, commit_sha, is_crystallized, crystal_id, 
-        created_at
-      FROM intent_logs 
-      WHERE type IN ('decision', 'system', 'fix', 'heritage', 'adr')
-      ORDER BY created_at DESC 
-      LIMIT ?
-    `,e)}create(e){let t=this.insert(`
-      INSERT INTO intent_logs (mission_id, symbol_id, file_path, type, content, confidence, symbol_name, signature, commit_sha)
-      VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?)
-    `,e.mission_id,e.symbol_id,e.file_path,e.type,e.content,e.confidence,e.symbol_name,e.signature,e.commit_sha);return s.EMBEDDABLE_TYPES.has(e.type)&&this.generateAndStoreEmbedding(Number(t),e).catch(i=>{d.debug({err:i,intentLogId:t},"Failed to generate intent log embedding")}),t}static EMBEDDABLE_TYPES=new Set(["decision","discovery","fix","blocker","note","heritage","crystal"]);static buildEmbeddingText(e){let t=[`[${e.type}]`];return e.symbol_name&&t.push(`symbol: ${e.symbol_name}`),e.file_path&&t.push(`file: ${e.file_path.split("/").pop()}`),t.push(e.content),t.join(" ")}async generateAndStoreEmbedding(e,t){let{generateEmbedding:i}=await Promise.resolve().then(()=>(L(),I)),n=s.buildEmbeddingText(t),r=await i(n);r&&this.run("UPDATE intent_logs SET embedding = ? WHERE id = ?",JSON.stringify(r),e)}findWithEmbeddings(){return this.all("SELECT * FROM intent_logs WHERE embedding IS NOT NULL AND type NOT IN ('system', 'lapsed')")}async findSemanticMatches(e,t,i){let{cosineSimilarity:n}=await Promise.resolve().then(()=>(L(),I)),r=this.findWithEmbeddings();if(r.length>5e3)return d.warn({count:r.length},"Intent log count exceeds brute-force vector scan limit (5000). Skipping semantic recall."),[];let c=[];for(let l of r)if(!(i&&l.symbol_id===i))try{let a=JSON.parse(l.embedding),o=n(e,a);o>.25&&c.push({id:l.id,mission_id:l.mission_id,type:l.type,content:l.content,symbol_name:l.symbol_name,file_path:l.file_path,similarity:o,created_at:l.created_at})}catch{}return c.sort((l,a)=>a.similarity-l.similarity).slice(0,t)}delete(e){this.run("DELETE FROM intent_logs WHERE id = ?",e)}update(e,t){let i=Object.keys(t);if(i.length===0)return;let n=i.map(c=>`${c} = ?`).join(", "),r=Object.values(t);r.push(e),this.run(`UPDATE intent_logs SET ${n} WHERE id = ?`,...r)}findRepairableOrphans(){return this.all(`
-      SELECT id, file_path, symbol_name, signature 
-      FROM intent_logs 
-      WHERE symbol_id IS NULL AND symbol_name IS NOT NULL
-    `)}findOrphans(){return this.all(`
-      SELECT il.id, il.symbol_id, il.file_path, il.symbol_name
-      FROM intent_logs il
-      WHERE (il.symbol_id IS NOT NULL AND NOT EXISTS (SELECT 1 FROM exports e WHERE e.id = il.symbol_id))
-         OR (il.symbol_id IS NULL AND il.type != 'lapsed' AND il.type != 'system' AND il.type != 'adr')
-    `)}findLogsForMissingFiles(){return this.all(`
-      SELECT il.id
-      FROM intent_logs il
-      WHERE il.file_path IS NOT NULL
-      AND NOT EXISTS (
-        SELECT 1 FROM files f WHERE f.path = il.file_path
-      )
-    `)}markAsLapsed(e){this.run(`
-      UPDATE intent_logs 
-      SET symbol_id = NULL, 
-          type = 'lapsed',
-          content = 'Lapsed: ' || content
-      WHERE id = ?
-    `,e)}importHeritage(e,t,i,n){this.run(`
-      INSERT INTO intent_logs (type, content, commit_sha, created_at, confidence, mission_id)
-      VALUES ('heritage', ?, ?, ?, ?, NULL)
-    `,e,t,i,n)}countByType(e){return this.get("SELECT COUNT(*) as count FROM intent_logs WHERE type = ?",e)?.count||0}findRawByMission(e){return this.all(`SELECT 
-        id, mission_id, symbol_id, file_path, type, content, confidence, 
-        symbol_name, signature, commit_sha, is_crystallized, crystal_id, 
-        created_at
-       FROM intent_logs
-       WHERE mission_id = ? AND is_crystallized = 0
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-       ORDER BY created_at ASC`,e)}findCrystalByMission(e){return this.get(`SELECT 
-        id, mission_id, symbol_id, file_path, type, content, confidence, 
-        symbol_name, signature, commit_sha, is_crystallized, crystal_id, 
-        created_at
-       FROM intent_logs
-       WHERE mission_id = ? AND type = 'crystal'
-       ORDER BY created_at DESC LIMIT 1`,e)}crystallize(e,t){return this.transaction(()=>{let i=this.insert(`INSERT INTO intent_logs (mission_id, type, content, confidence, is_crystallized, symbol_id, file_path, symbol_name, signature, commit_sha)
-         VALUES (?, 'crystal', ?, 1.0, 0, NULL, NULL, NULL, NULL, NULL)`,e,t);return this.run(`UPDATE intent_logs
-         SET is_crystallized = 1, crystal_id = ?
-         WHERE mission_id = ? AND is_crystallized = 0 AND id != ?
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-       WHERE symbol_id = ? AND mission_id IS NULL AND is_crystallized = 0
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-       ORDER BY created_at ASC`,e)}crystallizeBySymbol(e,t){return this.transaction(()=>{let i=this.insert(`INSERT INTO intent_logs (mission_id, symbol_id, type, content, confidence, is_crystallized, file_path, symbol_name, signature, commit_sha)
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-         SET is_crystallized = 1, crystal_id = ?
-         WHERE symbol_id = ? AND mission_id IS NULL AND is_crystallized = 0 AND id != ?
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-       WHERE mission_id IN (${t})
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-       FROM intent_logs
-       WHERE mission_id IN (${t})
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-        id, mission_id, symbol_id, file_path, type, content, confidence, 
-        symbol_name, signature, commit_sha, is_crystallized, crystal_id, 
-        created_at
-         FROM intent_logs
-         WHERE mission_id = ? AND is_crystallized = 0 AND type NOT IN ('adr', 'system', 'crystal', 'lapsed')
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-      VALUES (?, ?, unixepoch())
-      ON CONFLICT(section) DO UPDATE SET
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-        updated_at = excluded.updated_at
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-        VALUES (?, ?, unixepoch(), unixepoch())
-      `,e,t);let i=this.getClaim(e);if(!i)throw new Error(`Failed to hydrate claim after insert for file ${e}`);return{status:"claimed",claim:i}}catch{let i=this.getClaim(e);if(!i)throw new Error(`Failed to read existing claim for file ${e}`);return i.mission_id===t?(this.run("UPDATE file_claims SET updated_at = unixepoch() WHERE file_path = ?",e),{status:"already_claimed",claim:this.getClaim(e)??i}):{status:"conflict",claim:i}}}releaseFile(e,t){let i=this.getClaim(e);return i?t!==void 0&&i.mission_id!==t?{released:!1,reason:"not_owner",claim:i}:(this.run("DELETE FROM file_claims WHERE file_path = ?",e),{released:!0}):{released:!1,reason:"not_found"}}releaseAllForMission(e){return this.run("DELETE FROM file_claims WHERE mission_id = ?",e)}getClaim(e){return this.get(`
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-        fc.mission_id,
-        fc.claimed_at,
-        fc.updated_at,
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-        m.status AS mission_status,
-        m.git_branch AS mission_branch
-      FROM file_claims fc
-      LEFT JOIN missions m ON m.id = fc.mission_id
-      WHERE fc.file_path = ?
-    `,e)}getClaimsForMission(e){return this.all(`
-      SELECT
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-        fc.mission_id,
-        fc.claimed_at,
-        fc.updated_at,
-        m.name AS mission_name,
-        m.status AS mission_status,
-        m.git_branch AS mission_branch
-      FROM file_claims fc
-      LEFT JOIN missions m ON m.id = fc.mission_id
-      WHERE fc.mission_id = ?
-      ORDER BY fc.file_path ASC
-    `,e)}listClaims(){return this.all(`
-      SELECT
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-        fc.mission_id,
-        fc.claimed_at,
-        fc.updated_at,
-        m.name AS mission_name,
-        m.status AS mission_status,
-        m.git_branch AS mission_branch
-      FROM file_claims fc
-      LEFT JOIN missions m ON m.id = fc.mission_id
-      ORDER BY fc.updated_at DESC, fc.file_path ASC
-    `)}getClaimsByFiles(e){if(e.length===0)return[];let t=e.map(()=>"?").join(", ");return this.all(`
-      SELECT
-        fc.file_path,
-        fc.mission_id,
-        fc.claimed_at,
-        fc.updated_at,
-        m.name AS mission_name,
-        m.status AS mission_status,
-        m.git_branch AS mission_branch
-      FROM file_claims fc
-      LEFT JOIN missions m ON m.id = fc.mission_id
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-      ORDER BY fc.file_path ASC
-    `,...e)}};var ie=class{static repositoryCache=new Map;static getInstance(e){let t=this.repositoryCache.get(e);if(t){let r=F(e),c=t.files?.database,a=!t.intentLogs||!t.searchHistory||!t.missions||!t.hologram||!t.claims;if(c===r&&r.open&&!a)return t;this.repositoryCache.delete(e)}let i=F(e),n={files:new K(i),exports:new j(i),imports:new q(i),missions:new V(i),intentLogs:new J(i),configs:new Q(i),content:new X(i),searchHistory:new Z(i),hologram:new ee(i),claims:new te(i)};return this.repositoryCache.set(e,n),n}static closeInstance(e){this.repositoryCache.delete(e),Se(e)}static clearCache(e){this.repositoryCache.delete(e)}};L();var ze=new Set(["FunctionDeclaration","ClassDeclaration","TsInterfaceDeclaration","TsTypeAliasDeclaration","TsEnumDeclaration","HTTP Route","Socket Event","Pub/Sub Topic","function","class","interface","type","enum"]),Ye={"HTTP Route":0,"Socket Event":0,"Pub/Sub Topic":0,TsInterfaceDeclaration:1,TsTypeAliasDeclaration:1,TsEnumDeclaration:1,interface:1,type:1,enum:1,FunctionDeclaration:2,function:2,ClassDeclaration:3,class:3};function Ke(s,e,t=[]){let i=t.length>0?`${t.join(" > ")} > ${e.name}`:String(e.name),n=[`Symbol: ${e.name}`,`Kind: ${e.kind??"Unknown"}`,`Scope: ${i}`,`File: ${s}`];return e.signature&&n.push(`Signature: ${String(e.signature)}`),e.doc&&n.push(`Doc: ${String(e.doc)}`),n.join(`
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+      )`,$e)}};var ie=class s{static repositoryCache=new Map;static getInstance(e){let t=s.repositoryCache.get(e);if(t){let r=F(e),c=t.files?.database,a=!t.intentLogs||!t.searchHistory||!t.missions||!t.hologram||!t.claims;if(c===r&&r.open&&!a)return t;s.repositoryCache.delete(e)}let i=F(e),n={files:new V(i),exports:new G(i),imports:new Q(i),missions:new ee(i),intentLogs:new Z(i),configs:new q(i),content:new j(i),searchHistory:new te(i),hologram:new J(i),claims:new Y(i)};return s.repositoryCache.set(e,n),n}static closeInstance(e){s.repositoryCache.delete(e),Le(e)}static clearCache(e){s.repositoryCache.delete(e)}};S();var ze=new Set(["FunctionDeclaration","ClassDeclaration","TsInterfaceDeclaration","TsTypeAliasDeclaration","TsEnumDeclaration","HTTP Route","Socket Event","Pub/Sub Topic","function","class","interface","type","enum"]),Ke={"HTTP Route":0,"Socket Event":0,"Pub/Sub Topic":0,TsInterfaceDeclaration:1,TsTypeAliasDeclaration:1,TsEnumDeclaration:1,interface:1,type:1,enum:1,FunctionDeclaration:2,function:2,ClassDeclaration:3,class:3};function Ye(s,e,t=[]){let i=t.length>0?`${t.join(" > ")} > ${e.name}`:String(e.name),n=[`Symbol: ${e.name}`,`Kind: ${e.kind??"Unknown"}`,`Scope: ${i}`,`File: ${s}`];return e.signature&&n.push(`Signature: ${String(e.signature)}`),e.doc&&n.push(`Doc: ${String(e.doc)}`),n.join(`
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-`);try{b&&w(b,{status:"error"})}catch{}process.exit(1)});
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