milens 0.6.4 → 0.6.6

package/.agents/skills/parser/SKILL.md

@@ -5,42 +5,63 @@ description: Code intelligence for the parser area — symbols, dependencies, an
 
 # Parser
 
+## Working with this area
+When working with code in **parser/**, follow these mandatory safety rules:
+
+### Before editing any symbol in this area:
+1. Call `mcp_milens_impact({target: "<symbol>", repo: "<workspaceRoot>"})` — check blast radius
+2. If depth-1 dependents > 5 → **STOP and warn** before proceeding
+3. Call `mcp_milens_context({name: "<symbol>", repo: "<workspaceRoot>"})` — see all callers/callees
+
+### Before committing changes in this area:
+1. Call `mcp_milens_detect_changes({repo: "<workspaceRoot>"})` — verify scope
+2. If unexpected files changed → **STOP and report**
+
+### Key tools for this area:
+| Task | Tool |
+|---|---|
+| Find all references | `mcp_milens_context` |
+| Check edit safety | `mcp_milens_edit_check` |
+| Text search across files | `mcp_milens_grep` |
+| See file symbols | `mcp_milens_get_file_symbols` |
+
 ## Overview
 Contains 76 symbols (26 exported) across 15 files.
 
 ## Key Symbols
 - **`LangSpec`** [interface] (src/parser/extract.ts:6) — 30 refs
-- **`loadLanguage`** [function] (src/parser/loader.ts:21) — 10 refs
-- **`getParser`** [function] (src/parser/loader.ts:32) — 9 refs
-- **`extractFromTree`** [function] (src/parser/extract.ts:250) — 6 refs
+- **`loadLanguage`** [function] (src/parser/loader.ts:21) — 14 refs
+- **`getParser`** [function] (src/parser/loader.ts:32) — 13 refs
+- **`extractFromTree`** [function] (src/parser/extract.ts:250) — 8 refs
+- **`supportedExtensions`** [function] (src/parser/languages.ts:29) — 6 refs
 - **`extractHtmlScripts`** [function] (src/parser/lang-html.ts:33) — 5 refs
 - **`extractMarkdown`** [function] (src/parser/lang-md.ts:34) — 5 refs
+- **`spec`** [variable] (src/parser/lang-ts.ts:5) — 5 refs
 - **`extractVueScript`** [function] (src/parser/lang-vue.ts:18) — 5 refs
+- **`initTreeSitter`** [function] (src/parser/loader.ts:15) — 5 refs
+- **`clearQueryCache`** [function] (src/parser/extract.ts:67) — 4 refs
 - **`extractHtmlRefs`** [function] (src/parser/lang-html.ts:52) — 4 refs
 - **`extractVueTemplateRefs`** [function] (src/parser/lang-vue.ts:37) — 4 refs
+- **`langForFile`** [function] (src/parser/languages.ts:24) — 4 refs
 - **`spec`** [variable] (src/parser/lang-js.ts:5) — 3 refs
-- **`spec`** [variable] (src/parser/lang-ts.ts:5) — 3 refs
-- **`clearQueryCache`** [function] (src/parser/extract.ts:67) — 2 refs
-- **`spec`** [variable] (src/parser/lang-css.ts:5) — 2 refs
-- **`spec`** [variable] (src/parser/lang-go.ts:5) — 2 refs
-- **`spec`** [variable] (src/parser/lang-py.ts:5) — 2 refs
 
 ## Entry Points
 - **`LangSpec`** [interface] — 30 incoming references
-- **`loadLanguage`** [function] — 10 incoming references
-- **`getParser`** [function] — 9 incoming references
-- **`extractFromTree`** [function] — 6 incoming references
-- **`extractHtmlScripts`** [function] — 5 incoming references
+- **`loadLanguage`** [function] — 14 incoming references
+- **`getParser`** [function] — 13 incoming references
+- **`extractFromTree`** [function] — 8 incoming references
+- **`supportedExtensions`** [function] — 6 incoming references
 
 ## Dependencies
 - **root**: `CodeSymbol`, `RawImport`, `RawCall`, `RawHeritage`, `RawReExport`, `RawTypeBinding`, `RawAssignmentBinding`, `RawReturnType` (+4 more)
+- **test**: `lang`, `parser`
 - **analyzer**: `find`, `resolve`
 - **store**: `load`
 
 ## Used By
-- **analyzer**: `langForFile`, `getParser`, `loadLanguage`, `extractFromTree`, `clearQueryCache`, `extractVueScript`, `extractVueTemplateRefs`, `extractHtmlScripts` (+6 more)
+- **analyzer**: `langForFile`, `supportedExtensions`, `getParser`, `loadLanguage`, `extractFromTree`, `clearQueryCache`, `extractVueScript`, `extractVueTemplateRefs` (+6 more)
 - **server**: `getParser`, `loadLanguage`, `ALL_LANGS`
-- **test**: `getParser`, `loadLanguage`, `extractFromTree`, `extractVueScript`, `extractVueTemplateRefs`, `spec`, `extractHtmlScripts`, `extractHtmlRefs` (+2 more)
+- **test**: `getParser`, `loadLanguage`, `extractFromTree`, `extractVueScript`, `extractVueTemplateRefs`, `spec`, `extractHtmlScripts`, `extractHtmlRefs` (+7 more)
 
 ## Files
 - src/parser/extract.ts

package/.agents/skills/root/SKILL.md

@@ -5,45 +5,68 @@ description: Code intelligence for the root area — symbols, dependencies, and
 
 # Root
 
+## Working with this area
+When working with code in **root/**, follow these mandatory safety rules:
+
+### Before editing any symbol in this area:
+1. Call `mcp_milens_impact({target: "<symbol>", repo: "<workspaceRoot>"})` — check blast radius
+2. If depth-1 dependents > 5 → **STOP and warn** before proceeding
+3. Call `mcp_milens_context({name: "<symbol>", repo: "<workspaceRoot>"})` — see all callers/callees
+
+### Before committing changes in this area:
+1. Call `mcp_milens_detect_changes({repo: "<workspaceRoot>"})` — verify scope
+2. If unexpected files changed → **STOP and report**
+
+### Key tools for this area:
+| Task | Tool |
+|---|---|
+| Find all references | `mcp_milens_context` |
+| Check edit safety | `mcp_milens_edit_check` |
+| Text search across files | `mcp_milens_grep` |
+| See file symbols | `mcp_milens_get_file_symbols` |
+
 ## Overview
-Contains 257 symbols (206 exported) across 14 files.
+Contains 204 symbols (153 exported) across 13 files.
 
 ## Key Symbols
-- **`CodeSymbol`** [interface] (src/types.ts:8) — 30 refs
-- **`SymbolLink`** [interface] (src/types.ts:26) — 13 refs
-- **`isTestFile`** [function] (src/utils.ts:2) — 9 refs
+- **`CodeSymbol`** [interface] (src/types.ts:8) — 41 refs
+- **`SymbolLink`** [interface] (src/types.ts:26) — 21 refs
+- **`isTestFile`** [function] (src/utils.ts:2) — 11 refs
 - **`RawCall`** [interface] (src/types.ts:44) — 7 refs
 - **`RawImport`** [interface] (src/types.ts:35) — 6 refs
 - **`ExtractionResult`** [interface] (src/types.ts:60) — 6 refs
+- **`generateAgentsMd`** [function] (src/agents-md.ts:43) — 4 refs
+- **`computeMetrics`** [function] (src/metrics.ts:21) — 4 refs
+- **`formatMetricsReport`** [function] (src/metrics.ts:62) — 4 refs
+- **`MilensMetrics`** [interface] (src/metrics.ts:4) — 4 refs
+- **`generateSkills`** [function] (src/skills.ts:19) — 4 refs
 - **`RawHeritage`** [interface] (src/types.ts:52) — 4 refs
 - **`RawTypeBinding`** [interface] (src/types.ts:80) — 4 refs
 - **`RawAssignmentBinding`** [interface] (src/types.ts:88) — 4 refs
 - **`RawReturnType`** [interface] (src/types.ts:96) — 4 refs
-- **`RawCallResultBinding`** [interface] (src/types.ts:104) — 4 refs
-- **`RawReExport`** [interface] (src/types.ts:73) — 3 refs
-- **`Annotation`** [interface] (src/types.ts:138) — 3 refs
-- **`generateAgentsMd`** [function] (src/agents-md.ts:43) — 2 refs
-- **`computeMetrics`** [function] (src/metrics.ts:21) — 2 refs
 
 ## Entry Points
-- **`CodeSymbol`** [interface] — 30 incoming references
-- **`has`** [function] — 26 incoming references
-- **`SymbolLink`** [interface] — 13 incoming references
-- **`isTestFile`** [function] — 9 incoming references
+- **`CodeSymbol`** [interface] — 41 incoming references
+- **`has`** [function] — 30 incoming references
+- **`SymbolLink`** [interface] — 21 incoming references
+- **`isTestFile`** [function] — 11 incoming references
 - **`RawCall`** [interface] — 7 incoming references
 
 ## Dependencies
-- **store**: `Database`, `RepoRegistry`, `AnnotationStore`, `runDecayPass`, `getIncomingLinks`, `getAllSymbols`, `getCodebaseSummary`, `register` (+23 more)
+- **store**: `Database`, `RepoRegistry`, `AnnotationStore`, `runDecayPass`, `getIncomingLinks`, `getAllSymbols`, `getCodebaseSummary`, `register` (+25 more)
 - **analyzer**: `loadAliases`, `analyze`, `resolve`, `clear`
 - **server**: `startHttp`, `startStdio`, `HookManager`, `get`, `enableHook`, `loadConfig`, `saveConfig`, `disableHook`
 - **security**: `loadRules`, `auditDependencies`
+- **orchestrator**: `Orchestrator`, `subscribe`, `runAndFormat`
 - **scripts**: `outDir`
+- **test**: `dbPath`
 
 ## Used By
 - **analyzer**: `isTestFile`, `CodeSymbol`, `ExtractionResult`, `RawImport`, `RawCall`, `RawHeritage`, `RawReExport`, `RawTypeBinding` (+8 more)
+- **orchestrator**: `CodeSymbol`, `has`
 - **parser**: `CodeSymbol`, `RawImport`, `RawCall`, `RawHeritage`, `RawReExport`, `RawTypeBinding`, `RawAssignmentBinding`, `RawReturnType` (+4 more)
 - **store**: `Annotation`, `AnnotationKey`, `Session`, `EvolutionEvent`, `CodeSymbol`, `SymbolLink`, `RepoEntry`, `has` (+1 more)
-- **test**: `CodeSymbol`, `SymbolLink`, `RawImport`, `RawCall`, `RawHeritage`, `RawTypeBinding`, `RawAssignmentBinding`, `RawReturnType` (+2 more)
+- **test**: `generateAgentsMd`, `AnnotationKey`, `CodeSymbol`, `SymbolLink`, `computeMetrics`, `formatMetricsReport`, `MilensMetrics`, `RawImport` (+9 more)
 - **security**: `has`
 - **server**: `has`
 
@@ -53,8 +76,7 @@ Contains 257 symbols (206 exported) across 14 files.
 - CONTRIBUTING.md
 - DEPLOY.md
 - README.md
-- TODO.md
-- TODO2.md
+- milens-upgrade.md
 - src/agents-md.ts
 - src/cli.ts
 - src/metrics.ts

package/.agents/skills/scripts/SKILL.md

@@ -5,14 +5,34 @@ description: Code intelligence for the scripts area — symbols, dependencies, a
 
 # Scripts
 
+## Working with this area
+When working with code in **scripts/**, follow these mandatory safety rules:
+
+### Before editing any symbol in this area:
+1. Call `mcp_milens_impact({target: "<symbol>", repo: "<workspaceRoot>"})` — check blast radius
+2. If depth-1 dependents > 5 → **STOP and warn** before proceeding
+3. Call `mcp_milens_context({name: "<symbol>", repo: "<workspaceRoot>"})` — see all callers/callees
+
+### Before committing changes in this area:
+1. Call `mcp_milens_detect_changes({repo: "<workspaceRoot>"})` — verify scope
+2. If unexpected files changed → **STOP and report**
+
+### Key tools for this area:
+| Task | Tool |
+|---|---|
+| Find all references | `mcp_milens_context` |
+| Check edit safety | `mcp_milens_edit_check` |
+| Text search across files | `mcp_milens_grep` |
+| See file symbols | `mcp_milens_get_file_symbols` |
+
 ## Overview
 Contains 29 symbols (0 exported) across 1 files.
 
 ## Entry Points
-- **`run`** [function] — 22 incoming references
 - **`ROOT`** [variable] — 2 incoming references
 - **`outDir`** [variable] — 2 incoming references
 - **`resolveTargets`** [function] — 1 incoming references
+- **`run`** [function] — 1 incoming references
 - **`__dirname`** [variable] — 1 incoming references
 
 ## Dependencies
@@ -20,8 +40,6 @@ Contains 29 symbols (0 exported) across 1 files.
 
 ## Used By
 - **root**: `outDir`
-- **store**: `run`
-- **test**: `run`
 
 ## Files
 - scripts/build-standalone.mjs

package/.agents/skills/security/SKILL.md

@@ -5,32 +5,52 @@ description: Code intelligence for the security area — symbols, dependencies,
 
 # Security
 
+## Working with this area
+When working with code in **security/**, follow these mandatory safety rules:
+
+### Before editing any symbol in this area:
+1. Call `mcp_milens_impact({target: "<symbol>", repo: "<workspaceRoot>"})` — check blast radius
+2. If depth-1 dependents > 5 → **STOP and warn** before proceeding
+3. Call `mcp_milens_context({name: "<symbol>", repo: "<workspaceRoot>"})` — see all callers/callees
+
+### Before committing changes in this area:
+1. Call `mcp_milens_detect_changes({repo: "<workspaceRoot>"})` — verify scope
+2. If unexpected files changed → **STOP and report**
+
+### Key tools for this area:
+| Task | Tool |
+|---|---|
+| Find all references | `mcp_milens_context` |
+| Check edit safety | `mcp_milens_edit_check` |
+| Text search across files | `mcp_milens_grep` |
+| See file symbols | `mcp_milens_get_file_symbols` |
+
 ## Overview
 Contains 35 symbols (15 exported) across 2 files.
 
 ## Key Symbols
-- **`loadRules`** [function] (src/security/rules.ts:1044) — 4 refs
+- **`loadRules`** [function] (src/security/rules.ts:1044) — 6 refs
+- **`auditDependencies`** [function] (src/security/deps.ts:732) — 4 refs
+- **`detectEcosystem`** [function] (src/security/deps.ts:512) — 3 refs
+- **`parseDependencies`** [function] (src/security/deps.ts:524) — 3 refs
+- **`checkVulnerabilities`** [function] (src/security/deps.ts:687) — 3 refs
 - **`Ecosystem`** [type] (src/security/deps.ts:8) — 3 refs
-- **`auditDependencies`** [function] (src/security/deps.ts:732) — 2 refs
 - **`VulnerabilityReport`** [interface] (src/security/deps.ts:26) — 2 refs
-- **`detectEcosystem`** [function] (src/security/deps.ts:512) — 1 refs
-- **`parseDependencies`** [function] (src/security/deps.ts:524) — 1 refs
-- **`checkVulnerabilities`** [function] (src/security/deps.ts:687) — 1 refs
+- **`getRulesByCategory`** [function] (src/security/rules.ts:1051) — 2 refs
+- **`getRulesBySeverity`** [function] (src/security/rules.ts:1055) — 2 refs
 - **`SecurityCategory`** [type] (src/security/rules.ts:3) — 1 refs
 - **`Dependency`** [interface] (src/security/deps.ts:10) — 0 refs
 - **`Vulnerability`** [interface] (src/security/deps.ts:16) — 0 refs
-- **`getRulesByCategory`** [function] (src/security/rules.ts:1048) — 0 refs
-- **`getRulesBySeverity`** [function] (src/security/rules.ts:1052) — 0 refs
 - **`SecurityRule`** [interface] (src/security/rules.ts:14) — 0 refs
 - **`SecurityMatch`** [interface] (src/security/rules.ts:29) — 0 refs
 - **`SecurityReport`** [interface] (src/security/rules.ts:41) — 0 refs
 
 ## Entry Points
 - **`readManifest`** [function] — 6 incoming references
-- **`loadRules`** [function] — 4 incoming references
-- **`Ecosystem`** [type] — 3 incoming references
-- **`manifestExists`** [function] — 2 incoming references
-- **`parseSemver`** [function] — 2 incoming references
+- **`loadRules`** [function] — 6 incoming references
+- **`auditDependencies`** [function] — 4 incoming references
+- **`detectEcosystem`** [function] — 3 incoming references
+- **`parseDependencies`** [function] — 3 incoming references
 
 ## Dependencies
 - **root**: `has`
@@ -38,6 +58,7 @@ Contains 35 symbols (15 exported) across 2 files.
 ## Used By
 - **root**: `loadRules`, `auditDependencies`
 - **server**: `loadRules`
+- **test**: `detectEcosystem`, `parseDependencies`, `checkVulnerabilities`, `auditDependencies`, `loadRules`, `getRulesByCategory`, `getRulesBySeverity`
 
 ## Files
 - src/security/deps.ts

package/.agents/skills/server/SKILL.md

@@ -5,42 +5,69 @@ description: Code intelligence for the server area — symbols, dependencies, an
 
 # Server
 
+## Working with this area
+When working with code in **server/**, follow these mandatory safety rules:
+
+### Before editing any symbol in this area:
+1. Call `mcp_milens_impact({target: "<symbol>", repo: "<workspaceRoot>"})` — check blast radius
+2. If depth-1 dependents > 5 → **STOP and warn** before proceeding
+3. Call `mcp_milens_context({name: "<symbol>", repo: "<workspaceRoot>"})` — see all callers/callees
+
+### Before committing changes in this area:
+1. Call `mcp_milens_detect_changes({repo: "<workspaceRoot>"})` — verify scope
+2. If unexpected files changed → **STOP and report**
+
+### Key tools for this area:
+| Task | Tool |
+|---|---|
+| Find all references | `mcp_milens_context` |
+| Check edit safety | `mcp_milens_edit_check` |
+| Text search across files | `mcp_milens_grep` |
+| See file symbols | `mcp_milens_get_file_symbols` |
+
 ## Overview
-Contains 74 symbols (12 exported) across 4 files.
+Contains 94 symbols (16 exported) across 5 files.
 
 ## Key Symbols
-- **`HookConfig`** [interface] (src/server/hooks.ts:5) — 3 refs
-- **`HookManager`** [class] (src/server/hooks.ts:43) — 2 refs
-- **`SessionContext`** [interface] (src/server/hooks.ts:15) — 2 refs
-- **`registerAllPrompts`** [function] (src/server/mcp-prompts.ts:637) — 2 refs
-- **`createMcpServer`** [function] (src/server/mcp.ts:367) — 2 refs
-- **`startStdio`** [function] (src/server/mcp.ts:2289) — 2 refs
-- **`startHttp`** [function] (src/server/mcp.ts:2297) — 2 refs
-- **`generateTestPlan`** [function] (src/server/test-plan.ts:14) — 2 refs
-- **`defaultOnSessionStart`** [function] (src/server/hooks.ts:100) — 0 refs
-- **`defaultOnSessionEnd`** [function] (src/server/hooks.ts:164) — 0 refs
-- **`defaultOnPreCommit`** [function] (src/server/hooks.ts:227) — 0 refs
-- **`TestPlan`** [interface] (src/server/test-plan.ts:3) — 0 refs
+- **`HookManager`** [class] (src/server/hooks.ts:43) — 8 refs
+- **`HookConfig`** [interface] (src/server/hooks.ts:5) — 5 refs
+- **`defaultOnSessionStart`** [function] (src/server/hooks.ts:100) — 4 refs
+- **`defaultOnSessionEnd`** [function] (src/server/hooks.ts:164) — 4 refs
+- **`defaultOnPreCommit`** [function] (src/server/hooks.ts:227) — 4 refs
+- **`defaultOnFileChange`** [function] (src/server/hooks.ts:313) — 4 refs
+- **`defaultOnPreCompact`** [function] (src/server/hooks.ts:340) — 4 refs
+- **`defaultOnPostCompact`** [function] (src/server/hooks.ts:358) — 4 refs
+- **`SessionContext`** [interface] (src/server/hooks.ts:15) — 4 refs
+- **`registerAllPrompts`** [function] (src/server/mcp-prompts.ts:637) — 4 refs
+- **`createMcpServer`** [function] (src/server/mcp.ts:370) — 4 refs
+- **`generateTestPlan`** [function] (src/server/test-plan.ts:14) — 4 refs
+- **`FileWatcher`** [class] (src/server/watcher.ts:50) — 3 refs
+- **`startStdio`** [function] (src/server/mcp.ts:2717) — 2 refs
+- **`startHttp`** [function] (src/server/mcp.ts:2756) — 2 refs
 
 ## Entry Points
-- **`get`** [method] — 8 incoming references
-- **`loadConfig`** [method] — 3 incoming references
-- **`saveConfig`** [method] — 3 incoming references
-- **`HookConfig`** [interface] — 3 incoming references
-- **`HookManager`** [class] — 2 incoming references
+- **`get`** [method] — 9 incoming references
+- **`HookManager`** [class] — 8 incoming references
+- **`loadConfig`** [method] — 7 incoming references
+- **`HookConfig`** [interface] — 5 incoming references
+- **`defaultOnSessionStart`** [function] — 4 incoming references
 
 ## Dependencies
-- **store**: `Database`, `AnnotationStore`, `RepoRegistry`, `getCodebaseSummary`, `recall`, `close`, `getStats`, `getTestCoverage` (+33 more)
-- **analyzer**: `reviewPr`, `resolve`, `find`
+- **store**: `Database`, `AnnotationStore`, `RepoRegistry`, `runDecayPass`, `getCodebaseSummary`, `recall`, `close`, `getStats` (+37 more)
+- **analyzer**: `reviewPr`, `analyze`, `resolve`, `find`, `clear`
 - **parser**: `getParser`, `loadLanguage`, `ALL_LANGS`
 - **security**: `loadRules`
+- **orchestrator**: `Orchestrator`, `snapshot`, `compare`, `runAndFormat`
 - **root**: `has`
+- **test**: `dbPath`
 
 ## Used By
 - **root**: `startHttp`, `startStdio`, `HookManager`, `get`, `enableHook`, `loadConfig`, `saveConfig`, `disableHook`
+- **test**: `HookManager`, `HookConfig`, `defaultOnSessionStart`, `defaultOnSessionEnd`, `defaultOnPreCommit`, `defaultOnFileChange`, `defaultOnPreCompact`, `defaultOnPostCompact` (+10 more)
 
 ## Files
 - src/server/hooks.ts
 - src/server/mcp-prompts.ts
 - src/server/mcp.ts
 - src/server/test-plan.ts
+- src/server/watcher.ts

package/.agents/skills/store/SKILL.md

@@ -5,42 +5,64 @@ description: Code intelligence for the store area — symbols, dependencies, and
 
 # Store
 
+## Working with this area
+When working with code in **store/**, follow these mandatory safety rules:
+
+### Before editing any symbol in this area:
+1. Call `mcp_milens_impact({target: "<symbol>", repo: "<workspaceRoot>"})` — check blast radius
+2. If depth-1 dependents > 5 → **STOP and warn** before proceeding
+3. Call `mcp_milens_context({name: "<symbol>", repo: "<workspaceRoot>"})` — see all callers/callees
+
+### Before committing changes in this area:
+1. Call `mcp_milens_detect_changes({repo: "<workspaceRoot>"})` — verify scope
+2. If unexpected files changed → **STOP and report**
+
+### Key tools for this area:
+| Task | Tool |
+|---|---|
+| Find all references | `mcp_milens_context` |
+| Check edit safety | `mcp_milens_edit_check` |
+| Text search across files | `mcp_milens_grep` |
+| See file symbols | `mcp_milens_get_file_symbols` |
+
 ## Overview
-Contains 128 symbols (14 exported) across 5 files.
+Contains 135 symbols (15 exported) across 5 files.
 
 ## Key Symbols
-- **`Database`** [class] (src/store/db.ts:10) — 42 refs
-- **`AnnotationStore`** [class] (src/store/annotations.ts:10) — 14 refs
-- **`RepoRegistry`** [class] (src/store/registry.ts:18) — 6 refs
+- **`Database`** [class] (src/store/db.ts:10) — 77 refs
+- **`AnnotationStore`** [class] (src/store/annotations.ts:10) — 19 refs
+- **`RepoRegistry`** [class] (src/store/registry.ts:18) — 13 refs
+- **`runDecayPass`** [function] (src/store/confidence.ts:85) — 6 refs
 - **`buildEmbeddingText`** [function] (src/store/vectors.ts:250) — 4 refs
 - **`TfIdfProvider`** [class] (src/store/vectors.ts:44) — 4 refs
 - **`EmbeddingStore`** [class] (src/store/vectors.ts:170) — 4 refs
-- **`runDecayPass`** [function] (src/store/confidence.ts:84) — 2 refs
+- **`decayConfidence`** [function] (src/store/confidence.ts:22) — 3 refs
+- **`boostConfidence`** [function] (src/store/confidence.ts:6) — 2 refs
+- **`getStaleAnnotations`** [function] (src/store/confidence.ts:38) — 2 refs
+- **`promoteSecurityAnnotations`** [function] (src/store/confidence.ts:48) — 2 refs
+- **`autoPromote`** [function] (src/store/confidence.ts:106) — 2 refs
 - **`EmbeddingProvider`** [interface] (src/store/vectors.ts:15) — 2 refs
-- **`decayConfidence`** [function] (src/store/confidence.ts:21) — 1 refs
-- **`boostConfidence`** [function] (src/store/confidence.ts:4) — 0 refs
-- **`getStaleAnnotations`** [function] (src/store/confidence.ts:37) — 0 refs
-- **`promoteSecurityAnnotations`** [function] (src/store/confidence.ts:47) — 0 refs
 - **`NeuralProvider`** [class] (src/store/vectors.ts:122) — 0 refs
 - **`SimilarResult`** [interface] (src/store/vectors.ts:23) — 0 refs
 
 ## Entry Points
-- **`Database`** [class] — 42 incoming references
-- **`get`** [method] — 21 incoming references
-- **`close`** [method] — 16 incoming references
-- **`AnnotationStore`** [class] — 14 incoming references
+- **`Database`** [class] — 77 incoming references
+- **`close`** [method] — 30 incoming references
+- **`get`** [method] — 22 incoming references
+- **`AnnotationStore`** [class] — 19 incoming references
 - **`rowToSymbol`** [function] — 13 incoming references
 
 ## Dependencies
 - **root**: `Annotation`, `AnnotationKey`, `Session`, `EvolutionEvent`, `CodeSymbol`, `SymbolLink`, `RepoEntry`, `has` (+1 more)
-- **scripts**: `run`
 - **analyzer**: `find`, `resolve`
+- **test**: `dbPath`
 
 ## Used By
-- **root**: `Database`, `RepoRegistry`, `AnnotationStore`, `runDecayPass`, `getIncomingLinks`, `getAllSymbols`, `getCodebaseSummary`, `register` (+23 more)
-- **analyzer**: `Database`, `TfIdfProvider`, `EmbeddingStore`, `buildEmbeddingText`, `get`, `clear`, `isFileUpToDate`, `upsertFileHash` (+22 more)
-- **server**: `Database`, `AnnotationStore`, `RepoRegistry`, `getCodebaseSummary`, `recall`, `close`, `getStats`, `getTestCoverage` (+33 more)
-- **test**: `Database`, `RepoRegistry`, `TfIdfProvider`, `EmbeddingStore`, `buildEmbeddingText`, `close`, `insertSymbol`, `findSymbolByName` (+44 more)
+- **root**: `Database`, `RepoRegistry`, `AnnotationStore`, `runDecayPass`, `getIncomingLinks`, `getAllSymbols`, `getCodebaseSummary`, `register` (+25 more)
+- **analyzer**: `Database`, `TfIdfProvider`, `EmbeddingStore`, `buildEmbeddingText`, `get`, `clearFiles`, `clear`, `isFileUpToDate` (+23 more)
+- **orchestrator**: `Database`, `findSymbolByName`, `findUpstream`, `clear`, `getTestCoverageGaps`, `findDeadCode`, `close`
+- **server**: `Database`, `AnnotationStore`, `RepoRegistry`, `runDecayPass`, `getCodebaseSummary`, `recall`, `close`, `getStats` (+37 more)
+- **test**: `Database`, `AnnotationStore`, `RepoRegistry`, `boostConfidence`, `decayConfidence`, `getStaleAnnotations`, `promoteSecurityAnnotations`, `runDecayPass` (+76 more)
 - **apps**: `remove`, `Database`, `getCodebaseSummary`, `close`
 - **docs**: `remove`
 - **parser**: `load`

package/.agents/skills/test/SKILL.md

@@ -5,8 +5,28 @@ description: Code intelligence for the test area — symbols, dependencies, and
 
 # Test
 
+## Working with this area
+When working with code in **test/**, follow these mandatory safety rules:
+
+### Before editing any symbol in this area:
+1. Call `mcp_milens_impact({target: "<symbol>", repo: "<workspaceRoot>"})` — check blast radius
+2. If depth-1 dependents > 5 → **STOP and warn** before proceeding
+3. Call `mcp_milens_context({name: "<symbol>", repo: "<workspaceRoot>"})` — see all callers/callees
+
+### Before committing changes in this area:
+1. Call `mcp_milens_detect_changes({repo: "<workspaceRoot>"})` — verify scope
+2. If unexpected files changed → **STOP and report**
+
+### Key tools for this area:
+| Task | Tool |
+|---|---|
+| Find all references | `mcp_milens_context` |
+| Check edit safety | `mcp_milens_edit_check` |
+| Text search across files | `mcp_milens_grep` |
+| See file symbols | `mcp_milens_get_file_symbols` |
+
 ## Overview
-Contains 129 symbols (43 exported) across 31 files.
+Contains 195 symbols (43 exported) across 49 files.
 
 ## Key Symbols
 - **`User`** [interface] (test/fixtures/ts-project/src/models.ts:1) — 5 refs
@@ -26,18 +46,28 @@ Contains 129 symbols (43 exported) across 31 files.
 - **`UserController`** [class] (test/fixtures/ts-project/src/nest-sample.ts:18) — 1 refs
 
 ## Entry Points
+- **`lang`** [variable] — 12 incoming references
+- **`dbPath`** [function] — 10 incoming references
 - **`User`** [interface] — 5 incoming references
+- **`parser`** [variable] — 3 incoming references
 - **`createUser`** [function] — 2 incoming references
-- **`UserRole`** [type] — 2 incoming references
-- **`create_user`** [function] — 2 incoming references
-- **`User`** [class] — 2 incoming references
 
 ## Dependencies
-- **store**: `Database`, `RepoRegistry`, `TfIdfProvider`, `EmbeddingStore`, `buildEmbeddingText`, `close`, `insertSymbol`, `findSymbolByName` (+44 more)
-- **root**: `CodeSymbol`, `SymbolLink`, `RawImport`, `RawCall`, `RawHeritage`, `RawTypeBinding`, `RawAssignmentBinding`, `RawReturnType` (+2 more)
-- **parser**: `getParser`, `loadLanguage`, `extractFromTree`, `extractVueScript`, `extractVueTemplateRefs`, `spec`, `extractHtmlScripts`, `extractHtmlRefs` (+2 more)
-- **analyzer**: `resolveLinks`, `resolveLinksWithStats`, `reviewSymbol`, `scanFiles`, `generateTestPlan`, `findCoverageGaps`, `analyze`, `loadAliases` (+1 more)
-- **scripts**: `run`
+- **root**: `generateAgentsMd`, `AnnotationKey`, `CodeSymbol`, `SymbolLink`, `computeMetrics`, `formatMetricsReport`, `MilensMetrics`, `RawImport` (+9 more)
+- **store**: `Database`, `AnnotationStore`, `RepoRegistry`, `boostConfidence`, `decayConfidence`, `getStaleAnnotations`, `promoteSecurityAnnotations`, `runDecayPass` (+76 more)
+- **security**: `detectEcosystem`, `parseDependencies`, `checkVulnerabilities`, `auditDependencies`, `loadRules`, `getRulesByCategory`, `getRulesBySeverity`
+- **analyzer**: `enrichMetadata`, `resolveLinks`, `resolveLinksWithStats`, `reviewSymbol`, `reviewPr`, `scanFiles`, `generateTestPlan`, `findCoverageGaps` (+5 more)
+- **parser**: `getParser`, `loadLanguage`, `extractFromTree`, `extractVueScript`, `extractVueTemplateRefs`, `spec`, `extractHtmlScripts`, `extractHtmlRefs` (+7 more)
+- **server**: `HookManager`, `HookConfig`, `defaultOnSessionStart`, `defaultOnSessionEnd`, `defaultOnPreCommit`, `defaultOnFileChange`, `defaultOnPreCompact`, `defaultOnPostCompact` (+10 more)
+- **orchestrator**: `Orchestrator`, `formatReport`, `OrchestratorReport`, `subscribe`, `run`, `snapshot`, `compare`, `cancel` (+3 more)
+
+## Used By
+- **apps**: `dbPath`
+- **analyzer**: `parser`, `lang`
+- **root**: `dbPath`
+- **parser**: `lang`, `parser`
+- **server**: `dbPath`
+- **store**: `dbPath`
 
 ## Files
 - test/fixtures/go-project/models/user.go
@@ -59,15 +89,33 @@ Contains 129 symbols (43 exported) across 31 files.
 - test/fixtures/vue-project-refs/src/views/TestView.vue
 - test/fixtures/vue-project/src/composables/useClipboard.js
 - test/fixtures/vue-project/src/views/TestView.vue
+- test/unit/agents-md.test.ts
+- test/unit/annotations.test.ts
+- test/unit/cli.test.ts
+- test/unit/confidence.test.ts
 - test/unit/database.test.ts
 - test/unit/db-extended.test.ts
+- test/unit/deps-audit.test.ts
+- test/unit/enrich.test.ts
 - test/unit/extractor.test.ts
+- test/unit/hooks.test.ts
 - test/unit/html-css.test.ts
+- test/unit/languages.test.ts
 - test/unit/markdown.test.ts
+- test/unit/mcp-prompts.test.ts
+- test/unit/mcp-tools.test.ts
+- test/unit/metrics.test.ts
+- test/unit/orchestrator.test.ts
+- test/unit/parser-extract-cache.test.ts
+- test/unit/parser-loader.test.ts
 - test/unit/registry.test.ts
 - test/unit/resolver.test.ts
 - test/unit/review.test.ts
 - test/unit/scanner.test.ts
+- test/unit/security-rules.test.ts
+- test/unit/server-test-plan.test.ts
+- test/unit/skills.test.ts
 - test/unit/testplan.test.ts
+- test/unit/utils.test.ts
 - test/unit/vectors.test.ts
 - test/unit/vue-import.test.ts