milens 0.6.9 → 0.7.1

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

@@ -1,66 +1,62 @@
----
-name: milens-security
-description: Code intelligence for the security area — symbols, dependencies, and entry points
----
-
-# 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) — 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
-- **`VulnerabilityReport`** [interface] (src/security/deps.ts:26) — 2 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
-- **`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] — 6 incoming references
-- **`auditDependencies`** [function] — 4 incoming references
-- **`detectEcosystem`** [function] — 3 incoming references
-- **`parseDependencies`** [function] — 3 incoming references
-
-## Dependencies
-- **test**: `add`
-- **root**: `has`
-
-## Used By
-- **root**: `loadRules`, `auditDependencies`
-- **server**: `loadRules`
-- **test**: `detectEcosystem`, `parseDependencies`, `checkVulnerabilities`, `auditDependencies`, `loadRules`, `getRulesByCategory`, `getRulesBySeverity`
-
-## Files
-- src/security/deps.ts
-- src/security/rules.ts
+---
+name: milens-security
+description: Code intelligence for the security area — symbols, dependencies, and entry points
+---
+
+# 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 45 symbols (15 exported) across 2 files.
+
+## Key Symbols
+- **`loadRules`** [function] (src/security/rules.ts:1302) — 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
+- **`VulnerabilityReport`** [interface] (src/security/deps.ts:26) — 2 refs
+- **`getRulesByCategory`** [function] (src/security/rules.ts:1309) — 2 refs
+- **`getRulesBySeverity`** [function] (src/security/rules.ts:1313) — 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
+- **`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
+- **`loadRules`** [function] — 6 incoming references
+- **`auditDependencies`** [function] — 4 incoming references
+- **`detectEcosystem`** [function] — 3 incoming references
+- **`parseDependencies`** [function] — 3 incoming references
+
+## Used By
+- **root**: `loadRules`, `auditDependencies`
+- **server**: `loadRules`
+- **test**: `detectEcosystem`, `parseDependencies`, `checkVulnerabilities`, `auditDependencies`, `loadRules`, `getRulesByCategory`, `getRulesBySeverity`
+
+## Files
+- src/security/deps.ts
+- src/security/rules.ts

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

@@ -1,73 +1,77 @@
----
-name: milens-server
-description: Code intelligence for the server area — symbols, dependencies, and entry points
----
-
-# 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 99 symbols (16 exported) across 5 files.
-
-## Key Symbols
-- **`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:420) — 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:2907) — 2 refs
-- **`startHttp`** [function] (src/server/mcp.ts:2946) — 2 refs
-
-## Entry Points
-- **`get`** [method] — 12 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`, `runDecayPass`, `getCodebaseSummary`, `recall`, `close`, `getStats` (+36 more)
-- **analyzer**: `reviewPr`, `analyze`, `resolve`, `clear`
-- **parser**: `getParser`, `loadLanguage`, `ALL_LANGS`
-- **security**: `loadRules`
-- **orchestrator**: `Orchestrator`, `snapshot`, `compare`, `runAndFormat`
-- **root**: `has`
-- **test**: `add`, `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
+---
+name: milens-server
+description: Code intelligence for the server area — symbols, dependencies, and entry points
+---
+
+# 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 113 symbols (22 exported) across 10 files.
+
+## Key Symbols
+- **`HookManager`** [class] (src/server/hooks.ts:43) — 9 refs
+- **`Deps`** [interface] (src/server/tools/deps.ts:4) — 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
+- **`HookConfig`** [interface] (src/server/hooks.ts:5) — 5 refs
+- **`FileWatcher`** [class] (src/server/watcher.ts:50) — 5 refs
+- **`defaultOnPreCommit`** [function] (src/server/hooks.ts:237) — 4 refs
+- **`defaultOnFileChange`** [function] (src/server/hooks.ts:323) — 4 refs
+- **`SessionContext`** [interface] (src/server/hooks.ts:15) — 4 refs
+- **`registerAllPrompts`** [function] (src/server/mcp-prompts.ts:623) — 4 refs
+- **`createMcpServer`** [function] (src/server/mcp.ts:452) — 4 refs
+- **`startStdio`** [function] (src/server/mcp.ts:2306) — 4 refs
+- **`startHttp`** [function] (src/server/mcp.ts:2363) — 4 refs
+
+## Entry Points
+- **`HookManager`** [class] — 9 incoming references
+- **`Deps`** [interface] — 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`, `getStats`, `getTestCoverage` (+36 more)
+- **root**: `generateCrossRefSection`, `globToRegex`
+- **analyzer**: `reviewPr`, `countDependentFiles`, `analyze`
+- **parser**: `getParser`, `loadLanguage`, `ALL_LANGS`
+- **orchestrator**: `Orchestrator`, `loadSnapshots`, `snapshot`, `persistSnapshots`, `compare`, `runAndFormat`
+- **security**: `loadRules`
+
+## Used By
+- **root**: `startHttp`, `startStdio`, `HookManager`, `defaultOnSessionStart`, `defaultOnSessionEnd`, `defaultOnPreCompact`, `defaultOnPostCompact`, `enableHook` (+3 more)
+- **test**: `defaultOnSessionStart`, `defaultOnPreCompact`, `defaultOnSessionEnd`, `defaultOnPostCompact`, `HookManager`, `HookConfig`, `defaultOnPreCommit`, `defaultOnFileChange` (+19 more)
+
+## Files
+- 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/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

@@ -1,75 +1,72 @@
----
-name: milens-store
-description: Code intelligence for the store area — symbols, dependencies, and entry points
----
-
-# 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 135 symbols (15 exported) across 5 files.
-
-## Key Symbols
-- **`Database`** [class] (src/store/db.ts:10) — 79 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
-- **`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
-- **`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
-- **`NeuralProvider`** [class] (src/store/vectors.ts:122) — 0 refs
-- **`SimilarResult`** [interface] (src/store/vectors.ts:23) — 0 refs
-
-## Entry Points
-- **`Database`** [class] — 79 incoming references
-- **`close`** [method] — 31 incoming references
-- **`get`** [method] — 23 incoming references
-- **`AnnotationStore`** [class] — 19 incoming references
-- **`RepoRegistry`** [class] — 16 incoming references
-
-## Dependencies
-- **root**: `Annotation`, `AnnotationKey`, `Session`, `EvolutionEvent`, `CodeSymbol`, `SymbolLink`, `RepoEntry`, `has` (+1 more)
-- **test**: `add`, `dbPath`
-- **analyzer**: `resolve`
-
-## Used By
-- **root**: `Database`, `RepoRegistry`, `AnnotationStore`, `runDecayPass`, `getIncomingLinks`, `getAllSymbols`, `getCodebaseSummary`, `register` (+24 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` (+36 more)
-- **test**: `Database`, `AnnotationStore`, `RepoRegistry`, `boostConfidence`, `decayConfidence`, `getStaleAnnotations`, `promoteSecurityAnnotations`, `runDecayPass` (+77 more)
-- **apps**: `remove`, `getAnnotations`, `Database`, `getCodebaseSummary`, `close`
-- **docs**: `remove`
-- **parser**: `load`
-
-## Files
-- src/store/annotations.ts
-- src/store/confidence.ts
-- src/store/db.ts
-- src/store/registry.ts
-- src/store/vectors.ts
+---
+name: milens-store
+description: Code intelligence for the store area — symbols, dependencies, and entry points
+---
+
+# 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 139 symbols (15 exported) across 5 files.
+
+## Key Symbols
+- **`Database`** [class] (src/store/db.ts:10) — 80 refs
+- **`AnnotationStore`** [class] (src/store/annotations.ts:10) — 21 refs
+- **`RepoRegistry`** [class] (src/store/registry.ts:18) — 16 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:23) — 3 refs
+- **`boostConfidence`** [function] (src/store/confidence.ts:6) — 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
+- **`AnnotationStore`** [class] — 21 incoming references
+- **`RepoRegistry`** [class] — 16 incoming references
+- **`findSymbolById`** [method] — 14 incoming references
+- **`rowToSymbol`** [function] — 13 incoming references
+
+## Dependencies
+- **root**: `Annotation`, `AnnotationKey`, `Session`, `EvolutionEvent`, `CodeSymbol`, `SymbolLink`, `RepoEntry`
+
+## Used By
+- **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` (+36 more)
+- **test**: `Database`, `AnnotationStore`, `RepoRegistry`, `boostConfidence`, `decayConfidence`, `getStaleAnnotations`, `promoteSecurityAnnotations`, `runDecayPass` (+76 more)
+- **apps**: `remove`, `getAnnotations`, `Database`, `getCodebaseSummary`
+- **parser**: `load`
+
+## Files
+- src/store/annotations.ts
+- src/store/confidence.ts
+- src/store/db.ts
+- src/store/registry.ts
+- src/store/vectors.ts