milens 0.7.0 → 0.7.2

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

@@ -1,8 +1,10 @@
 ---
+generated-by: milens
 name: milens-root
 description: Code intelligence for the root area — symbols, dependencies, and entry points
 ---
 
+<!-- Generated by milens — safe to delete/regenerate -->
 # Root
 
 ## Working with this area
@@ -25,58 +27,57 @@ When working with code in **root/**, follow these mandatory safety rules:
 | Text search across files | `mcp_milens_grep` |
 | See file symbols | `mcp_milens_get_file_symbols` |
 
+### Edit-safety enforcement
+A `PreToolUse` hook (warn mode by default) reminds you if no milens safety check (`impact`/`context`/`overview`/`guard_edit_check`/`edit_check`/`smart_context`) was called before an `Edit`/`Write`/`MultiEdit`. Opt-in strict deny mode is available via `milens hooks guard-set-mode --mode strict`. Both modes consume the check after one edit. See `.milens/hook-state/config.json`. Known caveat: the underlying `PreToolUse` deny mechanism has at least one reliability issue (https://github.com/anthropics/claude-code/issues/4362).
+
 ## Overview
-Contains 242 symbols (164 exported) across 13 files.
+Contains 238 symbols (157 exported) across 12 files.
 
 ## Key Symbols
-- **`CodeSymbol`** [interface] (src/types.ts:8) — 53 refs
-- **`SymbolLink`** [interface] (src/types.ts:26) — 24 refs
-- **`RawCall`** [interface] (src/types.ts:44) — 15 refs
-- **`isTestFile`** [function] (src/utils.ts:2) — 12 refs
+- **`CodeSymbol`** [interface] (src/types.ts:8) — 52 refs
+- **`SymbolLink`** [interface] (src/types.ts:26) — 22 refs
+- **`RawCall`** [interface] (src/types.ts:45) — 18 refs
+- **`isTestFile`** [function] (src/utils.ts:4) — 10 refs
 - **`RawImport`** [interface] (src/types.ts:35) — 9 refs
-- **`RawHeritage`** [interface] (src/types.ts:52) — 7 refs
-- **`ExtractionResult`** [interface] (src/types.ts:60) — 6 refs
-- **`RawTypeBinding`** [interface] (src/types.ts:80) — 6 refs
-- **`RawAssignmentBinding`** [interface] (src/types.ts:88) — 6 refs
-- **`RawReturnType`** [interface] (src/types.ts:96) — 5 refs
-- **`RawCallResultBinding`** [interface] (src/types.ts:104) — 5 refs
-- **`AnalysisStats`** [interface] (src/types.ts:113) — 5 refs
+- **`RawHeritage`** [interface] (src/types.ts:59) — 7 refs
+- **`ExtractionResult`** [interface] (src/types.ts:67) — 6 refs
+- **`RawTypeBinding`** [interface] (src/types.ts:88) — 6 refs
+- **`RawAssignmentBinding`** [interface] (src/types.ts:96) — 6 refs
+- **`globToRegex`** [function] (src/utils.ts:16) — 6 refs
+- **`RawReturnType`** [interface] (src/types.ts:104) — 5 refs
+- **`RawCallResultBinding`** [interface] (src/types.ts:112) — 5 refs
+- **`AnalysisStats`** [interface] (src/types.ts:135) — 5 refs
 - **`generateAgentsMd`** [function] (src/agents-md.ts:93) — 4 refs
 - **`computeMetrics`** [function] (src/metrics.ts:21) — 4 refs
-- **`formatMetricsReport`** [function] (src/metrics.ts:62) — 4 refs
 
 ## Entry Points
-- **`CodeSymbol`** [interface] — 53 incoming references
-- **`has`** [function] — 50 incoming references
-- **`SymbolLink`** [interface] — 24 incoming references
-- **`RawCall`** [interface] — 15 incoming references
-- **`isTestFile`** [function] — 12 incoming references
+- **`CodeSymbol`** [interface] — 52 incoming references
+- **`SymbolLink`** [interface] — 22 incoming references
+- **`RawCall`** [interface] — 18 incoming references
+- **`isTestFile`** [function] — 10 incoming references
+- **`RawImport`** [interface] — 9 incoming references
 
 ## Dependencies
-- **store**: `Database`, `RepoRegistry`, `AnnotationStore`, `runDecayPass`, `getIncomingLinks`, `getAllSymbols`, `getCodebaseSummary`, `register` (+24 more)
-- **analyzer**: `loadAliases`, `analyze`, `resolve`, `clear`
+- **store**: `Database`, `RepoRegistry`, `AnnotationStore`, `runDecayPass`, `getIncomingLinks`, `getAllSymbols`, `getCodebaseSummary`, `findDbPath` (+22 more)
+- **analyzer**: `loadAliases`, `analyze`, `resolve`
 - **ui**: `createProgressReporter`, `finalize`
-- **server**: `startHttp`, `startStdio`, `HookManager`, `get`, `enableHook`, `loadConfig`, `saveConfig`, `disableHook`
+- **server**: `startHttp`, `startStdio`, `HookManager`, `defaultOnSessionStart`, `defaultOnSessionEnd`, `defaultOnPreCompact`, `defaultOnPostCompact`, `handleMarkChecked` (+6 more)
 - **security**: `loadRules`, `auditDependencies`
 - **orchestrator**: `Orchestrator`, `subscribe`, `runAndFormat`
-- **test**: `add`, `dbPath`
-- **scripts**: `version`, `outDir`, `root`
 
 ## Used By
 - **analyzer**: `isTestFile`, `CodeSymbol`, `ExtractionResult`, `RawImport`, `RawCall`, `RawHeritage`, `RawReExport`, `RawTypeBinding` (+8 more)
-- **orchestrator**: `CodeSymbol`, `has`
+- **orchestrator**: `CodeSymbol`
 - **parser**: `CodeSymbol`, `RawImport`, `RawCall`, `RawHeritage`, `RawReExport`, `RawTypeBinding`, `RawAssignmentBinding`, `RawReturnType` (+4 more)
-- **server**: `generateCrossRefSection`, `has`
-- **store**: `Annotation`, `AnnotationKey`, `Session`, `EvolutionEvent`, `CodeSymbol`, `SymbolLink`, `RepoEntry`, `has` (+1 more)
+- **server**: `generateCrossRefSection`, `globToRegex`
+- **store**: `Annotation`, `AnnotationKey`, `Session`, `EvolutionEvent`, `CodeSymbol`, `SymbolLink`, `RepoEntry`
 - **ui**: `AnalysisStats`
-- **test**: `generateAgentsMd`, `AnnotationKey`, `CodeSymbol`, `SymbolLink`, `computeMetrics`, `formatMetricsReport`, `MilensMetrics`, `RawImport` (+17 more)
-- **security**: `has`
+- **test**: `generateAgentsMd`, `AnnotationKey`, `CodeSymbol`, `SymbolLink`, `computeMetrics`, `formatMetricsReport`, `MilensMetrics`, `RawImport` (+18 more)
 
 ## Files
 - AGENTS.md
 - CLAUDE.md
 - CONTRIBUTING.md
-- DEPLOY.md
 - README.md
 - src/agents-md.ts
 - src/cli.ts

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

@@ -1,8 +1,10 @@
 ---
+generated-by: milens
 name: milens-scripts
 description: Code intelligence for the scripts area — symbols, dependencies, and entry points
 ---
 
+<!-- Generated by milens — safe to delete/regenerate -->
 # Scripts
 
 ## Working with this area
@@ -25,30 +27,30 @@ When working with code in **scripts/**, follow these mandatory safety rules:
 | Text search across files | `mcp_milens_grep` |
 | See file symbols | `mcp_milens_get_file_symbols` |
 
+### Edit-safety enforcement
+A `PreToolUse` hook (warn mode by default) reminds you if no milens safety check (`impact`/`context`/`overview`/`guard_edit_check`/`edit_check`/`smart_context`) was called before an `Edit`/`Write`/`MultiEdit`. Opt-in strict deny mode is available via `milens hooks guard-set-mode --mode strict`. Both modes consume the check after one edit. See `.milens/hook-state/config.json`. Known caveat: the underlying `PreToolUse` deny mechanism has at least one reliability issue (https://github.com/anthropics/claude-code/issues/4362).
+
 ## Overview
-Contains 47 symbols (0 exported) across 3 files.
+Contains 80 symbols (0 exported) across 7 files.
 
 ## Entry Points
-- **`root`** [variable] — 37 incoming references
-- **`version`** [variable] — 4 incoming references
-- **`ROOT`** [variable] — 2 incoming references
-- **`outDir`** [variable] — 2 incoming references
-- **`main`** [function] — 2 incoming references
+- **`ghApi`** [function] — 4 incoming references
+- **`exec`** [function] — 3 incoming references
+- **`branch`** [variable] — 3 incoming references
+- **`detectBreakingFromLabels`** [function] — 3 incoming references
+- **`fail`** [function] — 3 incoming references
 
 ## Dependencies
 - **analyzer**: `resolve`
-- **store**: `Database`, `getCodebaseSummary`, `close`
 
 ## Used By
-- **docs**: `main`
-- **analyzer**: `root`
-- **root**: `version`, `outDir`, `root`
-- **parser**: `root`
-- **security**: `version`
-- **server**: `root`
-- **test**: `root`
+- **apps**: `parseArgs`, `generatePrPayload`
 
 ## Files
 - scripts/build-standalone.mjs
-- scripts/generate-release-stats.js
-- scripts/update-docs.js
+- scripts/check-console.mjs
+- scripts/create-pr.cjs
+- scripts/gen-build-info.mjs
+- scripts/pr-generator.cjs
+- scripts/smoke-test.mjs
+- scripts/sync-version.mjs

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

@@ -1,8 +1,10 @@
 ---
+generated-by: milens
 name: milens-security
 description: Code intelligence for the security area — symbols, dependencies, and entry points
 ---
 
+<!-- Generated by milens — safe to delete/regenerate -->
 # Security
 
 ## Working with this area
@@ -25,8 +27,11 @@ When working with code in **security/**, follow these mandatory safety rules:
 | Text search across files | `mcp_milens_grep` |
 | See file symbols | `mcp_milens_get_file_symbols` |
 
+### Edit-safety enforcement
+A `PreToolUse` hook (warn mode by default) reminds you if no milens safety check (`impact`/`context`/`overview`/`guard_edit_check`/`edit_check`/`smart_context`) was called before an `Edit`/`Write`/`MultiEdit`. Opt-in strict deny mode is available via `milens hooks guard-set-mode --mode strict`. Both modes consume the check after one edit. See `.milens/hook-state/config.json`. Known caveat: the underlying `PreToolUse` deny mechanism has at least one reliability issue (https://github.com/anthropics/claude-code/issues/4362).
+
 ## Overview
-Contains 44 symbols (15 exported) across 2 files.
+Contains 47 symbols (17 exported) across 2 files.
 
 ## Key Symbols
 - **`loadRules`** [function] (src/security/rules.ts:1301) — 6 refs
@@ -35,6 +40,7 @@ Contains 44 symbols (15 exported) across 2 files.
 - **`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
+- **`ALL_RULES`** [variable] (src/security/rules.ts:99) — 3 refs
 - **`VulnerabilityReport`** [interface] (src/security/deps.ts:26) — 2 refs
 - **`getRulesByCategory`** [function] (src/security/rules.ts:1308) — 2 refs
 - **`getRulesBySeverity`** [function] (src/security/rules.ts:1312) — 2 refs
@@ -43,7 +49,6 @@ Contains 44 symbols (15 exported) across 2 files.
 - **`Vulnerability`** [interface] (src/security/deps.ts:16) — 0 refs
 - **`SecurityRule`** [interface] (src/security/rules.ts:31) — 0 refs
 - **`SecurityMatch`** [interface] (src/security/rules.ts:47) — 0 refs
-- **`SecurityReport`** [interface] (src/security/rules.ts:59) — 0 refs
 
 ## Entry Points
 - **`readManifest`** [function] — 6 incoming references
@@ -52,11 +57,6 @@ Contains 44 symbols (15 exported) across 2 files.
 - **`detectEcosystem`** [function] — 3 incoming references
 - **`parseDependencies`** [function] — 3 incoming references
 
-## Dependencies
-- **scripts**: `version`
-- **test**: `add`
-- **root**: `has`
-
 ## Used By
 - **root**: `loadRules`, `auditDependencies`
 - **server**: `loadRules`

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

@@ -1,8 +1,10 @@
 ---
+generated-by: milens
 name: milens-server
 description: Code intelligence for the server area — symbols, dependencies, and entry points
 ---
 
+<!-- Generated by milens — safe to delete/regenerate -->
 # Server
 
 ## Working with this area
@@ -25,50 +27,58 @@ When working with code in **server/**, follow these mandatory safety rules:
 | Text search across files | `mcp_milens_grep` |
 | See file symbols | `mcp_milens_get_file_symbols` |
 
+### Edit-safety enforcement
+A `PreToolUse` hook (warn mode by default) reminds you if no milens safety check (`impact`/`context`/`overview`/`guard_edit_check`/`edit_check`/`smart_context`) was called before an `Edit`/`Write`/`MultiEdit`. Opt-in strict deny mode is available via `milens hooks guard-set-mode --mode strict`. Both modes consume the check after one edit. See `.milens/hook-state/config.json`. Known caveat: the underlying `PreToolUse` deny mechanism has at least one reliability issue (https://github.com/anthropics/claude-code/issues/4362).
+
 ## Overview
-Contains 102 symbols (16 exported) across 5 files.
+Contains 154 symbols (37 exported) across 12 files.
 
 ## Key Symbols
-- **`HookManager`** [class] (src/server/hooks.ts:43) — 8 refs
+- **`Deps`** [interface] (src/server/tools/deps.ts:4) — 11 refs
+- **`HookManager`** [class] (src/server/hooks.ts:43) — 9 refs
+- **`defaultOnSessionStart`** [function] (src/server/hooks.ts:100) — 8 refs
+- **`defaultOnSessionEnd`** [function] (src/server/hooks.ts:174) — 8 refs
+- **`defaultOnPreCompact`** [function] (src/server/hooks.ts:350) — 8 refs
+- **`defaultOnPostCompact`** [function] (src/server/hooks.ts:368) — 8 refs
+- **`createMcpServer`** [function] (src/server/mcp.ts:452) — 6 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:174) — 4 refs
+- **`FileWatcher`** [class] (src/server/watcher.ts:50) — 5 refs
+- **`readMode`** [function] (src/server/guard-hook.ts:38) — 4 refs
+- **`writeMode`** [function] (src/server/guard-hook.ts:50) — 4 refs
+- **`handleMarkChecked`** [function] (src/server/guard-hook.ts:147) — 4 refs
+- **`handleCheckEdit`** [function] (src/server/guard-hook.ts:161) — 4 refs
 - **`defaultOnPreCommit`** [function] (src/server/hooks.ts:237) — 4 refs
 - **`defaultOnFileChange`** [function] (src/server/hooks.ts:323) — 4 refs
-- **`defaultOnPreCompact`** [function] (src/server/hooks.ts:350) — 4 refs
-- **`defaultOnPostCompact`** [function] (src/server/hooks.ts:368) — 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:451) — 4 refs
-- **`generateTestPlan`** [function] (src/server/test-plan.ts:39) — 4 refs
-- **`FileWatcher`** [class] (src/server/watcher.ts:50) — 3 refs
-- **`startStdio`** [function] (src/server/mcp.ts:2975) — 2 refs
-- **`startHttp`** [function] (src/server/mcp.ts:3014) — 2 refs
 
 ## Entry Points
-- **`get`** [method] — 13 incoming references
-- **`HookManager`** [class] — 8 incoming references
-- **`loadConfig`** [method] — 7 incoming references
-- **`HookConfig`** [interface] — 5 incoming references
-- **`defaultOnSessionStart`** [function] — 4 incoming references
+- **`Deps`** [interface] — 11 incoming references
+- **`HookManager`** [class] — 9 incoming references
+- **`defaultOnSessionStart`** [function] — 8 incoming references
+- **`defaultOnSessionEnd`** [function] — 8 incoming references
+- **`defaultOnPreCompact`** [function] — 8 incoming references
 
 ## Dependencies
-- **store**: `Database`, `AnnotationStore`, `RepoRegistry`, `runDecayPass`, `getCodebaseSummary`, `recall`, `close`, `getStats` (+36 more)
-- **root**: `generateCrossRefSection`, `has`
-- **analyzer**: `reviewPr`, `analyze`, `resolve`, `clear`
+- **store**: `Database`, `AnnotationStore`, `RepoRegistry`, `runDecayPass`, `getCodebaseSummary`, `recall`, `getStats`, `getTestCoverage` (+38 more)
+- **root**: `generateCrossRefSection`, `globToRegex`
+- **analyzer**: `reviewPr`, `countDependentFiles`, `analyze`
 - **parser**: `getParser`, `loadLanguage`, `ALL_LANGS`
-- **security**: `loadRules`
 - **orchestrator**: `Orchestrator`, `loadSnapshots`, `snapshot`, `persistSnapshots`, `compare`, `runAndFormat`
-- **test**: `add`, `dbPath`
-- **scripts**: `root`
+- **security**: `loadRules`
 
 ## Used By
-- **root**: `startHttp`, `startStdio`, `HookManager`, `get`, `enableHook`, `loadConfig`, `saveConfig`, `disableHook`
-- **test**: `HookManager`, `HookConfig`, `defaultOnSessionStart`, `defaultOnSessionEnd`, `defaultOnPreCommit`, `defaultOnFileChange`, `defaultOnPreCompact`, `defaultOnPostCompact` (+10 more)
+- **root**: `startHttp`, `startStdio`, `HookManager`, `defaultOnSessionStart`, `defaultOnSessionEnd`, `defaultOnPreCompact`, `defaultOnPostCompact`, `handleMarkChecked` (+6 more)
+- **test**: `defaultOnSessionStart`, `defaultOnPreCompact`, `defaultOnSessionEnd`, `defaultOnPostCompact`, `createMcpServer`, `markChecked`, `checkEdit`, `readMode` (+26 more)
 
 ## Files
+- src/server/guard-hook.ts
 - src/server/hooks.ts
 - src/server/mcp-prompts.ts
 - src/server/mcp.ts
 - src/server/test-plan.ts
+- src/server/tools/deps.ts
+- src/server/tools/findings-report.ts
+- src/server/tools/resources.ts
+- src/server/tools/security.ts
+- src/server/tools/session.ts
+- src/server/tools/testing.ts
 - src/server/watcher.ts

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

@@ -1,8 +1,10 @@
 ---
+generated-by: milens
 name: milens-store
 description: Code intelligence for the store area — symbols, dependencies, and entry points
 ---
 
+<!-- Generated by milens — safe to delete/regenerate -->
 # Store
 
 ## Working with this area
@@ -25,47 +27,46 @@ When working with code in **store/**, follow these mandatory safety rules:
 | Text search across files | `mcp_milens_grep` |
 | See file symbols | `mcp_milens_get_file_symbols` |
 
+### Edit-safety enforcement
+A `PreToolUse` hook (warn mode by default) reminds you if no milens safety check (`impact`/`context`/`overview`/`guard_edit_check`/`edit_check`/`smart_context`) was called before an `Edit`/`Write`/`MultiEdit`. Opt-in strict deny mode is available via `milens hooks guard-set-mode --mode strict`. Both modes consume the check after one edit. See `.milens/hook-state/config.json`. Known caveat: the underlying `PreToolUse` deny mechanism has at least one reliability issue (https://github.com/anthropics/claude-code/issues/4362).
+
 ## Overview
-Contains 135 symbols (15 exported) across 5 files.
+Contains 146 symbols (15 exported) across 5 files.
 
 ## Key Symbols
 - **`Database`** [class] (src/store/db.ts:10) — 80 refs
-- **`AnnotationStore`** [class] (src/store/annotations.ts:10) — 19 refs
-- **`RepoRegistry`** [class] (src/store/registry.ts:18) — 16 refs
-- **`runDecayPass`** [function] (src/store/confidence.ts:85) — 6 refs
+- **`AnnotationStore`** [class] (src/store/annotations.ts:10) — 21 refs
+- **`RepoRegistry`** [class] (src/store/registry.ts:24) — 18 refs
+- **`runDecayPass`** [function] (src/store/confidence.ts:87) — 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
-- **`decayConfidence`** [function] (src/store/confidence.ts:22) — 3 refs
+- **`decayConfidence`** [function] (src/store/confidence.ts:23) — 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
+- **`getStaleAnnotations`** [function] (src/store/confidence.ts:40) — 2 refs
+- **`promoteSecurityAnnotations`** [function] (src/store/confidence.ts:50) — 2 refs
+- **`autoPromote`** [function] (src/store/confidence.ts:108) — 2 refs
 - **`EmbeddingProvider`** [interface] (src/store/vectors.ts:15) — 2 refs
 - **`NeuralProvider`** [class] (src/store/vectors.ts:122) — 0 refs
 - **`SimilarResult`** [interface] (src/store/vectors.ts:23) — 0 refs
 
 ## Entry Points
 - **`Database`** [class] — 80 incoming references
-- **`close`** [method] — 33 incoming references
-- **`get`** [method] — 23 incoming references
-- **`AnnotationStore`** [class] — 19 incoming references
-- **`RepoRegistry`** [class] — 16 incoming references
+- **`AnnotationStore`** [class] — 21 incoming references
+- **`RepoRegistry`** [class] — 18 incoming references
+- **`findSymbolById`** [method] — 15 incoming references
+- **`rowToSymbol`** [function] — 13 incoming references
 
 ## Dependencies
-- **root**: `Annotation`, `AnnotationKey`, `Session`, `EvolutionEvent`, `CodeSymbol`, `SymbolLink`, `RepoEntry`, `has` (+1 more)
-- **test**: `add`, `dbPath`
-- **analyzer**: `resolve`
+- **root**: `Annotation`, `AnnotationKey`, `Session`, `EvolutionEvent`, `CodeSymbol`, `SymbolLink`, `RepoEntry`
 
 ## Used By
-- **root**: `Database`, `RepoRegistry`, `AnnotationStore`, `runDecayPass`, `getIncomingLinks`, `getAllSymbols`, `getCodebaseSummary`, `register` (+24 more)
-- **analyzer**: `Database`, `TfIdfProvider`, `EmbeddingStore`, `buildEmbeddingText`, `get`, `isFileUpToDate`, `upsertFileHash`, `getSymbolsByFile` (+22 more)
-- **orchestrator**: `Database`, `findSymbolByName`, `findUpstream`, `clear`, `getTestCoverageGaps`, `findDeadCode`, `close`
-- **server**: `Database`, `AnnotationStore`, `RepoRegistry`, `runDecayPass`, `getCodebaseSummary`, `recall`, `close`, `getStats` (+36 more)
-- **test**: `Database`, `AnnotationStore`, `RepoRegistry`, `boostConfidence`, `decayConfidence`, `getStaleAnnotations`, `promoteSecurityAnnotations`, `runDecayPass` (+77 more)
-- **apps**: `remove`, `getAnnotations`, `Database`, `getCodebaseSummary`, `close`
-- **docs**: `remove`
-- **scripts**: `Database`, `getCodebaseSummary`, `close`
+- **root**: `Database`, `RepoRegistry`, `AnnotationStore`, `runDecayPass`, `getIncomingLinks`, `getAllSymbols`, `getCodebaseSummary`, `findDbPath` (+22 more)
+- **analyzer**: `Database`, `TfIdfProvider`, `EmbeddingStore`, `buildEmbeddingText`, `isFileUpToDate`, `upsertFileHash`, `getSymbolsByFile`, `transaction` (+18 more)
+- **orchestrator**: `Database`, `findSymbolByName`, `findUpstream`, `getTestCoverageGaps`, `findDeadCode`
+- **server**: `Database`, `AnnotationStore`, `RepoRegistry`, `runDecayPass`, `getCodebaseSummary`, `recall`, `getStats`, `getTestCoverage` (+38 more)
+- **test**: `Database`, `AnnotationStore`, `RepoRegistry`, `boostConfidence`, `decayConfidence`, `getStaleAnnotations`, `promoteSecurityAnnotations`, `runDecayPass` (+76 more)
+- **apps**: `remove`, `getAnnotations`, `Database`, `getCodebaseSummary`
 - **parser**: `load`
 
 ## Files

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

@@ -1,8 +1,10 @@
 ---
+generated-by: milens
 name: milens-test
 description: Code intelligence for the test area — symbols, dependencies, and entry points
 ---
 
+<!-- Generated by milens — safe to delete/regenerate -->
 # Test
 
 ## Working with this area
@@ -25,17 +27,20 @@ When working with code in **test/**, follow these mandatory safety rules:
 | Text search across files | `mcp_milens_grep` |
 | See file symbols | `mcp_milens_get_file_symbols` |
 
+### Edit-safety enforcement
+A `PreToolUse` hook (warn mode by default) reminds you if no milens safety check (`impact`/`context`/`overview`/`guard_edit_check`/`edit_check`/`smart_context`) was called before an `Edit`/`Write`/`MultiEdit`. Opt-in strict deny mode is available via `milens hooks guard-set-mode --mode strict`. Both modes consume the check after one edit. See `.milens/hook-state/config.json`. Known caveat: the underlying `PreToolUse` deny mechanism has at least one reliability issue (https://github.com/anthropics/claude-code/issues/4362).
+
 ## Overview
-Contains 328 symbols (119 exported) across 77 files.
+Contains 353 symbols (119 exported) across 83 files.
 
 ## Key Symbols
 - **`User`** [class] (test/fixtures/accuracy/py-project/src/models.py:1) — 6 refs
 - **`Calculator`** [class] (test/fixtures/accuracy/js-project/src/calculator.js:1) — 5 refs
 - **`User`** [interface] (test/fixtures/ts-project/src/models.ts:1) — 5 refs
-- **`save`** [method] (test/fixtures/accuracy/py-project/src/models.py:14) — 4 refs
+- **`User`** [class] (test/fixtures/accuracy/ruby-project/src/models.rb:1) — 5 refs
 - **`User`** [interface] (test/fixtures/accuracy/ts-project/src/models.ts:1) — 3 refs
 - **`User`** [class] (test/fixtures/py-project/models.py:1) — 3 refs
-- **`User`** [class] (test/fixtures/accuracy/ruby-project/src/models.rb:1) — 3 refs
+- **`UserRepo`** [class] (test/fixtures/accuracy/ruby-project/src/models.rb:10) — 3 refs
 - **`createCalc`** [function] (test/fixtures/accuracy/js-project/src/calculator.js:6) — 2 refs
 - **`UserRepository`** [class] (test/fixtures/accuracy/ts-project/src/models.ts:12) — 2 refs
 - **`createUser`** [function] (test/fixtures/ts-project/src/models.ts:9) — 2 refs
@@ -43,35 +48,26 @@ Contains 328 symbols (119 exported) across 77 files.
 - **`UserService`** [class] (test/fixtures/ts-project/src/nest-sample.ts:27) — 2 refs
 - **`Save`** [method] (test/fixtures/accuracy/go-project/src/models/user.go:16) — 2 refs
 - **`UserRepo`** [class] (test/fixtures/accuracy/py-project/src/models.py:10) — 2 refs
-- **`UserService`** [class] (test/fixtures/accuracy/py-project/src/service.py:4) — 2 refs
+- **`save`** [method] (test/fixtures/accuracy/py-project/src/models.py:14) — 2 refs
 
 ## Entry Points
-- **`add`** [method] — 46 incoming references
-- **`lang`** [variable] — 12 incoming references
-- **`dbPath`** [function] — 10 incoming references
 - **`User`** [class] — 6 incoming references
 - **`Calculator`** [class] — 5 incoming references
+- **`User`** [interface] — 5 incoming references
+- **`User`** [class] — 5 incoming references
+- **`User`** [interface] — 3 incoming references
 
 ## Dependencies
-- **analyzer**: `analyze`, `loadAliases`, `getCachedTree`, `clearTreeCache`, `enrichMetadata`, `resolveLinksWithStats`, `resolveLinks`, `reviewSymbol` (+10 more)
-- **store**: `Database`, `AnnotationStore`, `RepoRegistry`, `boostConfidence`, `decayConfidence`, `getStaleAnnotations`, `promoteSecurityAnnotations`, `runDecayPass` (+77 more)
-- **root**: `generateAgentsMd`, `AnnotationKey`, `CodeSymbol`, `SymbolLink`, `computeMetrics`, `formatMetricsReport`, `MilensMetrics`, `RawImport` (+17 more)
+- **analyzer**: `analyze`, `loadAliases`, `getCachedTree`, `clearTreeCache`, `enrichMetadata`, `resolveLinksWithStats`, `resolveLinks`, `reviewSymbol` (+9 more)
+- **store**: `Database`, `AnnotationStore`, `RepoRegistry`, `boostConfidence`, `decayConfidence`, `getStaleAnnotations`, `promoteSecurityAnnotations`, `runDecayPass` (+76 more)
+- **root**: `generateAgentsMd`, `AnnotationKey`, `CodeSymbol`, `SymbolLink`, `computeMetrics`, `formatMetricsReport`, `MilensMetrics`, `RawImport` (+18 more)
+- **server**: `defaultOnSessionStart`, `defaultOnPreCompact`, `defaultOnSessionEnd`, `defaultOnPostCompact`, `createMcpServer`, `markChecked`, `checkEdit`, `readMode` (+26 more)
 - **security**: `detectEcosystem`, `parseDependencies`, `checkVulnerabilities`, `auditDependencies`, `loadRules`, `getRulesByCategory`, `getRulesBySeverity`
 - **parser**: `getParser`, `loadLanguage`, `extractFromTree`, `extractVueScript`, `extractVueTemplateRefs`, `extractVueCompositionApi`, `extractVueTemplateAst`, `spec` (+11 more)
-- **server**: `HookManager`, `HookConfig`, `defaultOnSessionStart`, `defaultOnSessionEnd`, `defaultOnPreCommit`, `defaultOnFileChange`, `defaultOnPreCompact`, `defaultOnPostCompact` (+10 more)
 - **orchestrator**: `Orchestrator`, `formatReport`, `OrchestratorReport`, `subscribe`, `run`, `snapshot`, `compare`, `cancel` (+3 more)
-- **scripts**: `root`
 
 ## Used By
-- **apps**: `add`, `dbPath`
-- **docs**: `add`
-- **root**: `add`, `dbPath`
-- **analyzer**: `add`, `parser`, `lang`
-- **orchestrator**: `add`
-- **parser**: `lang`, `add`, `parser`
-- **security**: `add`
-- **server**: `add`, `dbPath`
-- **store**: `add`, `dbPath`
+- **apps**: `create`
 
 ## Files
 - test/fixtures/accuracy/go-project/src/admin.go
@@ -116,6 +112,7 @@ Contains 328 symbols (119 exported) across 77 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/setup.ts
 - test/unit/accuracy.test.ts
 - test/unit/agents-md.test.ts
 - test/unit/annotations.test.ts
@@ -127,27 +124,32 @@ Contains 328 symbols (119 exported) across 77 files.
 - test/unit/engine.test.ts
 - test/unit/enrich.test.ts
 - test/unit/extractor.test.ts
+- test/unit/findings-report.test.ts
+- test/unit/guard-hook.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/mcp-transport.test.ts
 - test/unit/metrics.test.ts
 - test/unit/mro.test.ts
 - test/unit/orchestrator.test.ts
 - test/unit/parser-extract-cache.test.ts
 - test/unit/parser-loader.test.ts
+- test/unit/pr-generator.test.ts
 - test/unit/registry.test.ts
 - test/unit/resolver.test.ts
 - test/unit/review.test.ts
+- test/unit/risk.test.ts
 - test/unit/scanner.test.ts
 - test/unit/scope-resolver.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/uninstall.test.ts
 - test/unit/utils.test.ts
 - test/unit/vectors.test.ts
 - test/unit/vue-import.test.ts
+- test/unit/watcher.test.ts

package/.agents/skills/ui/SKILL.md

@@ -1,8 +1,10 @@
 ---
+generated-by: milens
 name: milens-ui
 description: Code intelligence for the ui area — symbols, dependencies, and entry points
 ---
 
+<!-- Generated by milens — safe to delete/regenerate -->
 # Ui
 
 ## Working with this area
@@ -25,6 +27,9 @@ When working with code in **ui/**, follow these mandatory safety rules:
 | Text search across files | `mcp_milens_grep` |
 | See file symbols | `mcp_milens_get_file_symbols` |
 
+### Edit-safety enforcement
+A `PreToolUse` hook (warn mode by default) reminds you if no milens safety check (`impact`/`context`/`overview`/`guard_edit_check`/`edit_check`/`smart_context`) was called before an `Edit`/`Write`/`MultiEdit`. Opt-in strict deny mode is available via `milens hooks guard-set-mode --mode strict`. Both modes consume the check after one edit. See `.milens/hook-state/config.json`. Known caveat: the underlying `PreToolUse` deny mechanism has at least one reliability issue (https://github.com/anthropics/claude-code/issues/4362).
+
 ## Overview
 Contains 10 symbols (3 exported) across 1 files.
 
@@ -44,7 +49,7 @@ Contains 10 symbols (3 exported) across 1 files.
 - **root**: `AnalysisStats`
 
 ## Used By
-- **analyzer**: `ProgressPhase`, `ProgressReporter`, `startPhase`, `tick`, `endPhase`, `done`, `finalize`
+- **analyzer**: `ProgressPhase`, `ProgressReporter`, `startPhase`, `tick`, `endPhase`, `finalize`
 - **root**: `createProgressReporter`, `finalize`
 
 ## Files

package/README.md

@@ -98,20 +98,29 @@ Then connect your editor:
 claude mcp add milens -- milens serve -p .
 ```
 
-Or in .mcp.json at plugin root:
+Or drop this in `.mcp.json` at your project root (equivalent, works the same in the CLI, VS Code extension, and desktop app):
 
-```bash
+```json
 {
   "mcpServers": {
     "milens": {
       "type": "stdio",
       "command": "milens",
-      "args": ["serve", "-p", "${workspaceFolder}"]
+      "args": ["serve", "-p", "."]
     }
   }
 }
 ```
 
+Or install as a plugin from the marketplace:
+
+```bash
+/plugin marketplace add fuze210699/milens
+/plugin install milens
+```
+
+See [adapters/README.md](adapters/README.md#claude-code--via-plugin-install-marketplace) for how this avoids the workspace-root pitfall that broke earlier plugin builds.
+
 <details>
 <summary><b>More editors</b> — Cursor, OpenCode, Codex, Gemini, Zed</summary>