@kaisers-io/refs 0.6.0 → 0.6.1

package/CHANGELOG.md

@@ -7,6 +7,45 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [0.6.1] - 2026-08-03
+
+### Fixed
+
+- `refs doctor`'s `skill` check no longer reports a skill that is installed and working as
+  missing. It only ever looked in `~/.claude/skills/refs` and `~/.codex/skills/refs`, but
+  `npx skills add kaisers-io/refs` — the documented installer — writes neither: it keeps one
+  real copy in a shared `.agents/skills/refs` directory and symlinks each agent's own
+  directory at it. A Claude Code user was rescued by that symlink; anyone without one — a
+  Codex-only user, or anyone whose install went to the current project rather than `$HOME` —
+  was told to install a skill they already had, and never saw the version comparison that
+  `0.6.0` made the point of this check. Five locations are now checked, in this order:
+  `~/.agents/skills/refs/SKILL.md` (`shared ~/.agents`), `$CLAUDE_CONFIG_DIR` or `~/.claude`
+  (`Claude Code`), `$CODEX_HOME` or `~/.codex` (`Codex`), `<cwd>/.agents/skills/refs`
+  (`project ./.agents`), and `<cwd>/.claude/skills/refs` (`project ./.claude`). The last two
+  are there because `skills add` installs into the current project unless `-g` is passed, and
+  implies `-y` when it runs inside an agent, so an agent-driven install never touches `$HOME`
+  at all — and because naming a single agent (`skills add … -a claude-code`) switches the
+  installer to copy mode, which skips the shared `.agents` directory entirely and writes only
+  that agent's own. Unlike its global counterpart, the project path takes no env override:
+  the installer hardcodes a relative `.claude/skills` there. Codex needs no counterpart at
+  all, being a universal agent whose project install lands in `./.agents` in every mode. The
+  locations are deduplicated by resolved real path, so the usual symlinked install is
+  reported once rather than once per agent, while two genuinely independent copies are both
+  compared and a problem in either wins.
+- `refs doctor`'s "skill not found" message no longer claims the skill is not installed, and
+  no longer names directories it did not search. That list of locations is best-effort and
+  cannot be otherwise: the paths are the `skills` installer's implementation detail rather
+  than a documented contract, the canonical directory has moved before, and 74 agents carry a
+  global skills directory of their own. A skill installed for some other agent still works
+  and is simply invisible here, so the `detail` now names the locations it searched and keeps
+  the install hint for the case where the skill really is missing. Those names are derived
+  from the paths actually resolved, so with `$CLAUDE_CONFIG_DIR` or `$CODEX_HOME` set the
+  message names the override rather than the `~/.claude`/`~/.codex` it replaced — an override
+  moves the search, it does not widen it, and pointing anyone at the directory the check just
+  skipped would be worse than saying nothing. It stays a `warn`, never a `fail` — the skill's
+  own capability gate compares `refs --version` against the pin in the file the agent already
+  loaded and depends on none of this.
+
 ## [0.6.0] - 2026-08-03
 
 ### Changed
@@ -254,7 +293,8 @@ trusted-publishing pipeline end to end.
   installed git hooks.
 - Agent skill (`skills/refs/`) documenting the investigate/add/maintain workflows.
 
-[Unreleased]: https://github.com/kaisers-io/refs/compare/v0.6.0...HEAD
+[Unreleased]: https://github.com/kaisers-io/refs/compare/v0.6.1...HEAD
+[0.6.1]: https://github.com/kaisers-io/refs/compare/v0.6.0...v0.6.1
 [0.6.0]: https://github.com/kaisers-io/refs/compare/v0.5.1...v0.6.0
 [0.5.1]: https://github.com/kaisers-io/refs/compare/v0.5.0...v0.5.1
 [0.5.0]: https://github.com/kaisers-io/refs/compare/v0.4.0...v0.5.0

package/dist/refs.mjs

@@ -347,7 +347,7 @@ sync_ttl = "1h"
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 `)}},jd=class{constructor(e,t){this.flags=e,this.description=t||``,this.required=e.includes(`<`),this.optional=e.includes(`[`),this.variadic=/\w\.\.\.[>\]]$/.test(e),this.mandatory=!1;let n=Pd(e);this.short=n.shortFlag,this.long=n.longFlag,this.negate=!1,this.long&&(this.negate=this.long.startsWith(`--no-`)),this.defaultValue=void 0,this.defaultValueDescription=void 0,this.presetArg=void 0,this.envVar=void 0,this.parseArg=void 0,this.hidden=!1,this.argChoices=void 0,this.conflictsWith=[],this.implied=void 0,this.helpGroupHeading=void 0}default(e,t){return this.defaultValue=e,this.defaultValueDescription=t,this}preset(e){return this.presetArg=e,this}conflicts(e){return this.conflictsWith=this.conflictsWith.concat(e),this}implies(e){let t=e;return typeof e==`string`&&(t={[e]:!0}),this.implied=Object.assign(this.implied||{},t),this}env(e){return this.envVar=e,this}argParser(e){return this.parseArg=e,this}makeOptionMandatory(e=!0){return this.mandatory=!!e,this}hideHelp(e=!0){return this.hidden=!!e,this}_collectValue(e,t){return t===this.defaultValue||!Array.isArray(t)?[e]:(t.push(e),t)}choices(e){return this.argChoices=e.slice(),this.parseArg=(e,t)=>{if(!this.argChoices.includes(e))throw new Dd(`Allowed choices are ${this.argChoices.join(`, `)}.`);return this.variadic?this._collectValue(e,t):e},this}name(){return this.long?this.long.replace(/^--/,``):this.short.replace(/^-/,``)}attributeName(){return this.negate?Nd(this.name().replace(/^no-/,``)):Nd(this.name())}helpGroup(e){return this.helpGroupHeading=e,this}is(e){return this.short===e||this.long===e}isBoolean(){return!this.required&&!this.optional&&!this.negate}},Md=class{constructor(e){this.positiveOptions=new Map,this.negativeOptions=new Map,this.dualOptions=new Set,e.forEach(e=>{e.negate?this.negativeOptions.set(e.attributeName(),e):this.positiveOptions.set(e.attributeName(),e)}),this.negativeOptions.forEach((e,t)=>{this.positiveOptions.has(t)&&this.dualOptions.add(t)})}valueFromOption(e,t){let n=t.attributeName();if(!this.dualOptions.has(n))return!0;let r=this.negativeOptions.get(n).presetArg,i=r!==void 0&&r;return t.negate===(i===e)}};function Nd(e){return e.split(`-`).reduce((e,t)=>e+t[0].toUpperCase()+t.slice(1))}function Pd(e){let t,n,r=/^-[^-]$/,i=/^--[^-]/,a=e.split(/[ |,]+/).concat(`guard`);if(r.test(a[0])&&(t=a.shift()),i.test(a[0])&&(n=a.shift()),!t&&r.test(a[0])&&(t=a.shift()),!t&&i.test(a[0])&&(t=n,n=a.shift()),a[0].startsWith(`-`)){let t=a[0],n=`option creation failed due to '${t}' in option flags '${e}'`;throw/^-[^-][^-]/.test(t)?Error(`${n}
@@ -365,6 +365,6 @@ Expecting one of '${n.join(`', '`)}'`);return this._lifeCycleHooks[e]?this._life
  - if the default executable name is not suitable, use the executableFile option to supply a custom name or path
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o=n.includes(p.extname(i)),s;h.platform===`win32`?(this._checkForMissingExecutable(i,a,e._name),t.unshift(i),t=Rd(h.execArgv).concat(t),s=ge.spawn(h.execPath,t,{stdio:`inherit`})):o?(t.unshift(i),t=Rd(h.execArgv).concat(t),s=ge.spawn(h.argv[0],t,{stdio:`inherit`})):s=ge.spawn(i,t,{stdio:`inherit`}),s.killed||[`SIGUSR1`,`SIGUSR2`,`SIGTERM`,`SIGINT`,`SIGHUP`].forEach(e=>{h.on(e,()=>{s.killed===!1&&s.exitCode===null&&s.kill(e)})});let c=this._exitCallback;s.on(`close`,e=>{e??=1,c?c(new Ed(e,`commander.executeSubCommandAsync`,`(close)`)):h.exit(e)}),s.on(`error`,t=>{if(t.code===`ENOENT`)this._checkForMissingExecutable(i,a,e._name);else if(t.code===`EACCES`)throw Error(`'${i}' not executable`);if(!c)h.exit(1);else{let e=new Ed(1,`commander.executeSubCommandAsync`,`(error)`);e.nestedError=t,c(e)}}),this.runningCommand=s}_dispatchSubcommand(e,t,n){let r=this._findCommand(e);r||this.help({error:!0}),r._prepareForParse();let i;return i=this._chainOrCallSubCommandHook(i,r,`preSubcommand`),i=this._chainOrCall(i,()=>{if(r._executableHandler)this._executeSubCommand(r,t.concat(n));else return r._parseCommand(t,n)}),i}_dispatchHelpCommand(e){e||this.help();let t=this._findCommand(e);return t&&!t._executableHandler&&t.help(),this._dispatchSubcommand(e,[],[this._getHelpOption()?.long??this._getHelpOption()?.short??`--help`])}_checkNumberOfArguments(){this.registeredArguments.forEach((e,t)=>{e.required&&this.args[t]==null&&this.missingArgument(e.name())}),!(this.registeredArguments.length>0&&this.registeredArguments[this.registeredArguments.length-1].variadic)&&this.args.length>this.registeredArguments.length&&this._excessArguments(this.args)}_processArguments(){let e=(e,t,n)=>{let r=t;if(t!==null&&e.parseArg){let i=`error: command-argument value '${t}' is invalid for argument '${e.name()}'.`;r=this._callParseArg(e,t,n,i)}return r};this._checkNumberOfArguments();let t=[];this.registeredArguments.forEach((n,r)=>{let i=n.defaultValue;n.variadic?r<this.args.length?(i=this.args.slice(r),n.parseArg&&(i=i.reduce((t,r)=>e(n,r,t),n.defaultValue))):i===void 0&&(i=[]):r<this.args.length&&(i=this.args[r],n.parseArg&&(i=e(n,i,n.defaultValue))),t[r]=i}),this.processedArgs=t}_chainOrCall(e,t){return e?.then&&typeof e.then==`function`?e.then(()=>t()):t()}_chainOrCallHooks(e,t){let n=e,r=[];return this._getCommandAndAncestors().reverse().filter(e=>e._lifeCycleHooks[t]!==void 0).forEach(e=>{e._lifeCycleHooks[t].forEach(t=>{r.push({hookedCommand:e,callback:t})})}),t===`postAction`&&r.reverse(),r.forEach(e=>{n=this._chainOrCall(n,()=>e.callback(e.hookedCommand,this))}),n}_chainOrCallSubCommandHook(e,t,n){let r=e;return this._lifeCycleHooks[n]!==void 0&&this._lifeCycleHooks[n].forEach(e=>{r=this._chainOrCall(r,()=>e(this,t))}),r}_parseCommand(e,t){let n=this.parseOptions(t);if(this._parseOptionsEnv(),this._parseOptionsImplied(),e=e.concat(n.operands),t=n.unknown,this.args=e.concat(t),e&&this._findCommand(e[0]))return this._dispatchSubcommand(e[0],e.slice(1),t);if(this._getHelpCommand()&&e[0]===this._getHelpCommand().name())return this._dispatchHelpCommand(e[1]);if(this._defaultCommandName)return this._outputHelpIfRequested(t),this._dispatchSubcommand(this._defaultCommandName,e,t);this.commands.length&&this.args.length===0&&!this._actionHandler&&!this._defaultCommandName&&this.help({error:!0}),this._outputHelpIfRequested(n.unknown),this._checkForMissingMandatoryOptions(),this._checkForConflictingOptions();let r=()=>{n.unknown.length>0&&this.unknownOption(n.unknown[0])},i=`command:${this.name()}`;if(this._actionHandler){r(),this._processArguments();let n;return n=this._chainOrCallHooks(n,`preAction`),n=this._chainOrCall(n,()=>this._actionHandler(this.processedArgs)),this.parent&&(n=this._chainOrCall(n,()=>{this.parent.emit(i,e,t)})),n=this._chainOrCallHooks(n,`postAction`),n}if(this.parent?.listenerCount(i))r(),this._processArguments(),this.parent.emit(i,e,t);else if(e.length){if(this._findCommand(`*`))return this._dispatchSubcommand(`*`,e,t);this.listenerCount(`command:*`)?this.emit(`command:*`,e,t):this.commands.length?this.unknownCommand():(r(),this._processArguments())}else this.commands.length?(r(),this.help({error:!0})):(r(),this._processArguments())}_findCommand(e){if(e)return this.commands.find(t=>t._name===e||t._aliases.includes(e))}_findOption(e){return this.options.find(t=>t.is(e))}_checkForMissingMandatoryOptions(){this._getCommandAndAncestors().forEach(e=>{e.options.forEach(t=>{t.mandatory&&e.getOptionValue(t.attributeName())===void 0&&e.missingMandatoryOptionValue(t)})})}_checkForConflictingLocalOptions(){let e=this.options.filter(e=>{let t=e.attributeName();return this.getOptionValue(t)!==void 0&&this.getOptionValueSource(t)!=="default"});e.filter(e=>e.conflictsWith.length>0).forEach(t=>{let n=e.find(e=>t.conflictsWith.includes(e.attributeName()));n&&this._conflictingOption(t,n)})}_checkForConflictingOptions(){this._getCommandAndAncestors().forEach(e=>{e._checkForConflictingLocalOptions()})}parseOptions(e){let t=[],n=[],r=t;function i(e){return e.length>1&&e[0]===`-`}let a=e=>/^-(\d+|\d*\.\d+)(e[+-]?\d+)?$/.test(e)?!this._getCommandAndAncestors().some(e=>e.options.map(e=>e.short).some(e=>/^-\d$/.test(e))):!1,o=null,s=null,c=0;for(;c<e.length||s;){let l=s??e[c++];if(s=null,l===`--`){r===n&&r.push(l),r.push(...e.slice(c));break}if(o&&(!i(l)||a(l))){this.emit(`option:${o.name()}`,l);continue}if(o=null,i(l)){let t=this._findOption(l);if(t){if(t.required){let n=e[c++];n===void 0&&this.optionMissingArgument(t),this.emit(`option:${t.name()}`,n)}else if(t.optional){let n=null;c<e.length&&(!i(e[c])||a(e[c]))&&(n=e[c++]),this.emit(`option:${t.name()}`,n)}else this.emit(`option:${t.name()}`);o=t.variadic?t:null;continue}}if(l.length>2&&l[0]===`-`&&l[1]!==`-`){let e=this._findOption(`-${l[1]}`);if(e){e.required||e.optional&&this._combineFlagAndOptionalValue?this.emit(`option:${e.name()}`,l.slice(2)):(this.emit(`option:${e.name()}`),s=`-${l.slice(2)}`);continue}}if(/^--[^=]+=/.test(l)){let e=l.indexOf(`=`),t=this._findOption(l.slice(0,e));if(t&&(t.required||t.optional)){this.emit(`option:${t.name()}`,l.slice(e+1));continue}}if(r===t&&i(l)&&!(this.commands.length===0&&a(l))&&(r=n),(this._enablePositionalOptions||this._passThroughOptions)&&t.length===0&&n.length===0){if(this._findCommand(l)){t.push(l),n.push(...e.slice(c));break}else if(this._getHelpCommand()&&l===this._getHelpCommand().name()){t.push(l,...e.slice(c));break}else if(this._defaultCommandName){n.push(l,...e.slice(c));break}}if(this._passThroughOptions){r.push(l,...e.slice(c));break}r.push(l)}return{operands:t,unknown:n}}opts(){if(this._storeOptionsAsProperties){let e={},t=this.options.length;for(let n=0;n<t;n++){let t=this.options[n].attributeName();e[t]=t===this._versionOptionName?this._version:this[t]}return e}return this._optionValues}optsWithGlobals(){return this._getCommandAndAncestors().reduce((e,t)=>Object.assign(e,t.opts()),{})}error(e,t){this._outputConfiguration.outputError(`${e}\n`,this._outputConfiguration.writeErr),typeof this._showHelpAfterError==`string`?this._outputConfiguration.writeErr(`${this._showHelpAfterError}\n`):this._showHelpAfterError&&(this._outputConfiguration.writeErr(`
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$s(n,{...t,refs:{...t.refs,[s]:l.updated}}),{field:r,key:s,new:eg(l.new),old:eg(l.old)}})},_g=`settings`,vg=[],yg=()=>Object.keys(is.shape).toSorted().join(`, `),bg=e=>`unknown setting '${e}' — valid settings: ${yg()}`,xg=e=>Object.hasOwn(is.shape,e),Sg=e=>`note: 'settings' addressed the global settings, not ${e} — use the full ref key to edit that ref`,Cg=e=>{try{let t=Sp(e,_g);return[Sg(`ref '${t}'`)]}catch(e){if(e instanceof _&&e.code===`usage`)return[Sg("one of several matching refs — see `refs list`")];if(e instanceof _&&e.code===`not_found`)return vg;throw e}},wg=e=>({data:{field:e.key,key:_g,new:eg(e.parsed[e.key]),old:eg(e.old)},warnings:Cg(e.config)}),Tg=(e,t)=>{let n=H(e.env);return J(n,`home`,async()=>{let e=await W(n);if(!xg(t.key))throw y(bg(t.key));let r=e.settings[t.key],i={...e.settings,[t.key]:t.value},a=is.safeParse(i);if(!a.success)throw b(O(a.error));return await $s(n,{...e,settings:a.data}),wg({config:e,key:t.key,old:r,parsed:a.data})})},Eg=[],Dg=e=>{let t={};return e.package!==void 0&&(t.packageName=e.package),t},Og=async(e,t)=>{if(t.first===`settings`){if(t.opts.packageName!==void 0)throw y(`--package is not valid with 'refs edit settings ...' — it only applies to ref/package edits`);return Tg(e,{key:t.second,value:t.value})}return{data:await gg(e,{field:t.second,opts:t.opts,query:t.first,value:t.value}),warnings:Eg}},kg=e=>e==null?`(unset)`:String(e),Ag=e=>[`${e.key}: ${e.field} '${kg(e.old)}' -> '${kg(e.new)}'`],jg=(e,t)=>{e.command(`edit`).description(`Edit one field: 'refs edit settings <key> <value>' for a global setting, or 'refs edit <ref> <field> <value> [--package <name>]' for a ref or package field.`).argument(`<ref-or-settings>`,`a ref key/unique suffix, or the literal 'settings'`).argument(`<field-or-key>`,`field to edit (or, in settings mode, the setting key)`).argument(`<value>`,`the new value`).option(`--package <name>`,`edit this package's field instead of a top-level ref field`).action((e,n,r,i,a)=>{let o=Z(a);return $(t,o,async()=>{let{data:a,warnings:s}=await Og(t,{first:e,opts:Dg(i),second:n,value:r});Q(t,o,Ag(a),a,s)})()})},Mg=`Install the agent skill: npx skills add kaisers-io/refs   (private phase: npx skills add <path-to-this-repo> --skill refs)`,Ng=async e=>{await a(e.root,{recursive:!0}),await a(e.sourcesDir,{recursive:!0}),await a(e.locksDir,{recursive:!0}),await a(e.hooksDir,{recursive:!0})},Pg=async e=>{let t=H(e.env);return await Ng(t),{config:await J(t,`home`,async()=>{let e=await lc(t,Cd);return await Mc(t),e}),home:t.root,skill_hint:Mg}},Fg=[(e,t)=>{e.command(`init`).description(`Seed or migrate the refs home directory, its config, and the git hooks guard.`).action((e,n)=>{let r=Z(n);return $(t,r,async()=>{let e=await Pg(t);Q(t,r,[`refs home: ${e.home} (${e.config})`,Mg],e)})()})},$h,jg,Cp,...uh],Ig=(e,t)=>{for(let n of Fg)n(e,t)},Lg=[``,`Examples:`,`  $ refs list --json`,`  $ refs sync --stale-only --json`,`  $ refs resolve zod/mini --json`,``,`Every command accepts --json for structured output and --verbose for stack traces on error.`].join(`
+`),Rg=new Set([`commander.help`,`commander.helpDisplayed`,`commander.version`]),zg=`--json`,Bg=`--verbose`,Vg=/\n$/u,Hg=/^error: /u,Ug=e=>e.replace(Hg,``),Wg=(e,t)=>{for(let n of e){if(n===`--`)return!1;if(n===t)return!0}return!1},Gg=e=>Wg(e,zg),Kg=e=>Wg(e,Bg),qg=(e,t,n)=>n&&t!==void 0?`${e}\n${t}`:e,Jg=e=>{let t=new Ld().name(`refs`).description(`Manage git-based reference checkouts shared across a workspace.`).version(Cd).option(zg,`emit machine-readable JSON on stdout instead of human-readable text`).option(Bg,`include stack traces in error output`).allowExcessArguments(!1).exitOverride().configureOutput({outputError:()=>{},writeErr:t=>{e.errLine(t.replace(Vg,``))},writeOut:t=>{e.out(t.replace(Vg,``))}});return t.addHelpText(`after`,Lg),Ig(t,e),t},Yg=()=>{process.exitCode=g.OK},Xg=(e,t,n)=>{Wd(e,t,{code:`usage`,message:qg(Ug(n.message),n.stack,t.verbose)}),process.exitCode=g.USAGE},Zg=(e,t,n)=>{if(Rg.has(n.code)){Yg();return}Xg(e,t,n)},Qg=(e,t,n)=>{let r=xe(n,{verbose:t.verbose});Wd(e,t,r),process.exitCode=r.exitCode},$g=async(e,t,n)=>{let r={json:Gg(n),verbose:Kg(n)};try{await t.parseAsync(n)}catch(t){if(t instanceof Ed){Zg(e,r,t);return}Qg(e,r,t)}},e_=(e,t)=>$g(e,Jg(e),t);import.meta.main&&await e_(Td(),process.argv);export{Jg as buildProgram,Z as cliOptsOf,Q as emit,Wd as emitError,Ud as errorMessageOf,Gd as progress,Td as realContext,Ig as registerCommands,e_ as run,$g as runProgram,Hd as warningsFor,$ as wrapAction};

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@kaisers-io/refs",
-  "version": "0.6.0",
+  "version": "0.6.1",
   "description": "Managed read-only git checkouts of reference repositories for coding agents.",
   "keywords": [
     "ai",