@porast1/mcp-cognitive 1.1.0 → 2.1.0

package/AGENT_INSTRUCTIONS.md

@@ -10,45 +10,32 @@
 The project uses an MCP server (`mcp-cognitive`) backed by Weaviate hybrid search for persistent AI knowledge.
 Facts survive between sessions — recall them before searching the codebase.
 
-### Tool Inventory (18 tools)
-
-#### CRUD — Core Knowledge
-
-| Tool               | When to use                                                                                               | Key params                                                                                                                       |
-| ------------------ | --------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------- |
-| `cognitive_recall` | **At task start** — before codebase research. Search facts by semantic query, filter by module/tags/type. | `query?` (optional — omit for filter-only), `module?`, `modules?` (multi-module parallel), `tags?`, `types?`, `agent?`, `limit?` |
-| `cognitive_store`  | After discovering an insight worth remembering. Use `dryRun=true` first to check for duplicates.          | `fact`, `type` (invariant/policy/convention/observation/ephemeral), `module`, `citations?`, `tags?`, `confidence?`, `dryRun?`    |
-| `cognitive_update` | To patch an existing fact in-place (confidence, tags, citations). Preserves ID and history.               | `id` (UUID), `confidence?`, `type?`, `module?`, `tags?`, `addTags?`, `removeTags?`, `citations?`                                 |
-| `cognitive_forget` | To archive outdated/incorrect facts (soft-delete with reason).                                            | `id` (UUID), `reason`                                                                                                            |
-
-#### Search & Discovery
-
-| Tool                              | When to use                                                          | Key params                                                                       |
-| --------------------------------- | -------------------------------------------------------------------- | -------------------------------------------------------------------------------- |
-| `cognitive_search_documents`      | Find indexed docs (DDD, architecture, guides).                       | `query`, `docType?`, `module?`, `project?`                                       |
-| `cognitive_search_code_artifacts` | Find indexed code by semantic meaning or keyword.                    | `query`, `module?`, `layer?`, `artifactType?`                                    |
-| `cognitive_search_test_artifacts` | Find indexed tests by description or module.                         | `query`, `module?`, `testType?`                                                  |
-| `cognitive_correlate`             | Cross-collection traceability: docs ↔ code ↔ tests. Gap detection. | `sourceId` or `sourceQuery`, `sourceCollection`, `targetCollections?`, `module?` |
-
-#### Indexing
-
-| Tool                            | When to use                                           | Key params                                                   |
-| ------------------------------- | ----------------------------------------------------- | ------------------------------------------------------------ |
-| `cognitive_store_document`      | Index a markdown doc chunk (auto-dedup via checksum). | `content`, `filePath`, `docType`, `project`, `checksum`      |
-| `cognitive_store_code_artifact` | Index a TypeScript file with metadata.                | `content`, `filePath`, `project`, `artifactType`, `checksum` |
-| `cognitive_store_test_artifact` | Index a test file with describe/it blocks.            | `content`, `filePath`, `project`, `testType`, `checksum`     |
-
-#### Analysis & Maintenance
-
-| Tool                 | When to use                                                                              | Key params                                         |
-| -------------------- | ---------------------------------------------------------------------------------------- | -------------------------------------------------- |
-| `cognitive_reason`   | Need a synthesized answer, not raw facts. Groups by module/type, detects contradictions. | `question`, `modules?`, `depth?` (shallow/deep)    |
-| `cognitive_timeline` | Review what was learned during a period. Chronological, grouped by day.                  | `since?`, `until?`, `module?`, `status?`, `order?` |
-| `cognitive_stats`    | Quick overview before deciding what to do. Counts, top tags, activity.                   | `module?`                                          |
-| `cognitive_verify`   | After refactors — check if citation file paths still exist.                              | `factId?` (omit = verify all)                      |
-| `cognitive_audit`    | Periodic quality check. Finds stale facts, broken citations, duplicates. Expensive.      | _(no params)_                                      |
-| `cognitive_compact`  | Merge duplicate facts. Preview first, then execute.                                      | `mode` (preview/execute), `factIdA?`, `factIdB?`   |
-| `cognitive_health`   | Check Weaviate infrastructure is running.                                                | _(no params)_                                      |
+### Tool Inventory (v2 — 5 unified tools)
+
+#### Core Tools (daily use)
+
+| Tool               | When to use                                                                                     | Key params                                                                                                                       |
+| ------------------ | ----------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------- |
+| `cognitive_recall` | **At task start** — search facts, docs, code, tests. Hybrid semantic + keyword, cross-encoder. | `query?`, `scope?` (all/facts/docs/code/tests), `module?`, `modules?`, `types?`, `tags?`, `agent?`, `docType?`, `layer?`, `testType?` |
+| `cognitive_store`  | After discovering an insight. Create, update, or archive facts with a single tool.              | **Create:** `fact`, `type`, `module`, `citations?`, `tags?`, `dryRun?`. **Update:** `id` + fields. **Archive:** `id`, `archive: true`, `reason` |
+
+#### Sync Tool (batch operations)
+
+| Tool              | When to use                                                                  | Key params                                           |
+| ----------------- | ---------------------------------------------------------------------------- | ---------------------------------------------------- |
+| `cognitive_sync`  | Sync docs/code/tests from `.cognitive/sync.json`. Or sync a single file.    | `project`, `scope?` (all/docs/code/tests), `filePath?`, `dryRun?` |
+
+#### Analysis Tool (periodic use)
+
+| Tool                | When to use                                                                      | Key params                                                                   |
+| ------------------- | -------------------------------------------------------------------------------- | ---------------------------------------------------------------------------- |
+| `cognitive_analyze` | Cross-collection correlation (docs↔code↔tests) or structured reasoning.         | **correlate:** `action: "correlate"`, `sourceCollection`, `sourceQuery`/`sourceId`. **reason:** `action: "reason"`, `question`, `depth?` |
+
+#### Admin Tool (maintenance)
+
+| Tool              | When to use                                                  | Key params                                                |
+| ----------------- | ------------------------------------------------------------ | --------------------------------------------------------- |
+| `cognitive_admin` | Infrastructure health, stats, audit, compact, verify, timeline | `action` (health/stats/audit/compact/verify/timeline) + action-specific params |
 
 ### Workflow Rules
 
@@ -61,8 +48,8 @@ Facts survive between sessions — recall them before searching the codebase.
    - `convention` (0.85–0.9) — team conventions, audit every 6 months
    - `observation` (0.7–0.8) — debugging insights, re-verify in 30 days
    - `ephemeral` (any) — temporary notes, auto-expire in 7 days
-5. **Update > Supersede** — use `cognitive_update` to patch facts. Only use `store({ supersedes })` when the fact text itself changed fundamentally.
-6. **Forget with reason** — when archiving, always explain why so the knowledge graph stays auditable.
+5. **Update via `cognitive_store`** — use `cognitive_store({ id: "uuid", ... })` to patch existing facts. Use `supersedes` only when the fact text changed fundamentally.
+6. **Archive with reason** — use `cognitive_store({ id: "uuid", archive: true, reason: "..." })` so the knowledge graph stays auditable.
 
 ### Example: Typical Agent Flow
 

package/README.md

@@ -2,7 +2,7 @@
 
 Universal [MCP](https://modelcontextprotocol.io/) server that gives AI agents persistent, searchable memory backed by [Weaviate](https://weaviate.io/) hybrid search (BM25 keyword + vector embeddings + cross-encoder reranking).
 
-Store facts, documents, code artifacts, and test artifacts. Query them with semantic search, filter by module/type/tags, reason across knowledge, detect contradictions, and keep the database healthy — all from 18 MCP tools.
+Store facts, documents, code artifacts, and test artifacts. Query them with semantic search, filter by module/type/tags, reason across knowledge, detect contradictions, and keep the database healthy — all from 5 unified MCP tools.
 
 ## Why
 
@@ -12,7 +12,7 @@ LLM agents lose context between sessions.
 - **Hybrid search** — BM25 keyword matching + transformer vector embeddings + reranking. Not just text search.
 - **Multi-tenancy** — one Weaviate instance, many projects. Data fully isolated via `WEAVIATE_TENANT`.
 - **4 collections** — `CognitiveFact`, `DocumentChunk`, `CodeArtifact`, `TestArtifact`. Facts, docs, code, tests.
-- **18 MCP tools** — CRUD, search, reasoning, audit, correlation, compaction, timeline, stats.
+- **5 unified MCP tools** — recall, store, sync, analyze, admin. Consolidated from 18 v1 tools for cleaner agent interaction.
 - **Agent profiles** — tune recall per agent role (architect vs. tester vs. debugger).
 - **Pattern detection** — auto-detect conventions from git diffs via post-commit hooks.
 - **Zero vendor lock-in** — port/adapter architecture. Weaviate is the sole adapter today.
@@ -71,7 +71,7 @@ Then add to `.vscode/mcp.json` (or copy from `.cognitive/mcp.jsonc`):
 
 ### 4. Done
 
-The MCP server registers 18 tools automatically. Your AI agent can now store and recall knowledge.
+The MCP server registers 5 unified tools automatically. Your AI agent can now store and recall knowledge.
 
 ---
 
@@ -94,45 +94,87 @@ Full reference in [`config/.env.example`](config/.env.example). Key variables:
 
 ---
 
-## Tools Reference
+## Tools Reference (v2 — 5 unified tools)
 
-### Core Knowledge (CRUD)
+> **v2.0.0** consolidated 18 v1 tools into 5 unified tools. Old v1 tool names are preserved in `src/tools/v1/` for reference.
 
-| Tool               | Description                                                                                                      |
-| ------------------ | ---------------------------------------------------------------------------------------------------------------- |
-| `cognitive_store`  | Store a new fact. Supports `dryRun=true` to check for duplicates before writing.                                 |
-| `cognitive_recall` | Hybrid search facts. Query is optional (filter-only mode). Supports `modules[]` for multi-module parallel query. |
-| `cognitive_update` | Patch a fact in-place (confidence, tags, citations, module, type). Supports incremental `addTags`/`removeTags`.  |
-| `cognitive_forget` | Archive (soft-delete) a fact with a reason.                                                                      |
+### `cognitive_recall` — Unified search across all collections
 
-### Search & Discovery
+Search facts, documents, code artifacts, and test artifacts with a single tool. Uses hybrid BM25 + vector search with cross-encoder reranking.
 
-| Tool                              | Description                                                                        |
-| --------------------------------- | ---------------------------------------------------------------------------------- |
-| `cognitive_search_documents`      | Hybrid search across indexed document chunks (DDD docs, architecture, guides).     |
-| `cognitive_search_code_artifacts` | Semantic search across indexed TypeScript code (entities, use cases, ports).       |
-| `cognitive_search_test_artifacts` | Semantic search across indexed tests (unit, integration, E2E).                     |
-| `cognitive_correlate`             | Cross-collection correlation: docs ↔ code ↔ tests. Gap detection & traceability. |
+| Param | Description |
+|-------|-------------|
+| `query` | Semantic or keyword search query. Optional for `scope: "facts"` (filter-only browsing). |
+| `scope` | `"all"` (default) \| `"facts"` \| `"docs"` \| `"code"` \| `"tests"` |
+| `module` | Filter by bounded context / module |
+| `modules` | Multi-module parallel query (OR logic) |
+| `types` | Filter by fact types (facts scope only) |
+| `tags` | Filter by tags — all must match (facts scope only) |
+| `agent` | Agent name for profile-based filtering |
+| `docType` | `"DDD"`, `"ARCHITECTURE"`, `"GUIDE"`, `"README"` (docs scope only) |
+| `layer` | `"domain"`, `"application"`, `"infrastructure"` (code scope only) |
+| `artifactType` | `"entity"`, `"usecase"`, `"port"`, `"adapter"` (code scope only) |
+| `testType` | `"unit"`, `"integration"`, `"e2e"` (tests scope only) |
+| `limit` | Max results per scope (default: 10) |
 
-### Indexing
+**Examples:**
+```
+cognitive_recall({ query: "cross-BC isolation rules" })
+cognitive_recall({ query: "Email value object", scope: "code", module: "identity" })
+cognitive_recall({ scope: "facts", tags: ["architecture"], types: ["invariant"] })
+```
+
+### `cognitive_store` — Create, update, or archive facts
+
+Unified fact management replacing `store`, `update`, and `forget`.
+
+| Mode | Params | Description |
+|------|--------|-------------|
+| **Create** | `fact`, `type`, `module`, `citations?`, `tags?`, `confidence?`, `dryRun?` | Store a new fact. Use `dryRun: true` to check for duplicates first. |
+| **Update** | `id`, + any patch fields (`confidence?`, `addTags?`, `removeTags?`, `type?`, `module?`) | Patch existing fact in-place. |
+| **Archive** | `id`, `archive: true`, `reason` | Soft-delete with audit trail. |
+
+**Examples:**
+```
+cognitive_store({ fact: "Domain must be pure TS", type: "invariant", module: "architecture", citations: ["ARCH.md:L97"] })
+cognitive_store({ id: "uuid", confidence: 0.95, addTags: ["verified"] })
+cognitive_store({ id: "uuid", archive: true, reason: "outdated after refactor" })
+```
 
-| Tool                            | Description                                                  |
-| ------------------------------- | ------------------------------------------------------------ |
-| `cognitive_store_document`      | Index a document chunk with checksum-based change detection. |
-| `cognitive_store_code_artifact` | Index a TypeScript code artifact with AST metadata.          |
-| `cognitive_store_test_artifact` | Index a test file with describe/it block metadata.           |
+### `cognitive_sync` — Batch & single-file synchronization
+
+Sync documents, code artifacts, and test artifacts into the knowledge base.
+
+| Mode | Params | Description |
+|------|--------|-------------|
+| **Batch** | `project`, `scope?` (`"all"` \| `"docs"` \| `"code"` \| `"tests"`) | Sync all files from `.cognitive/sync.json` config. |
+| **Single-file** | `project`, `filePath` | Auto-detects collection from file extension. |
+
+Supports `dryRun: true` for preview. Uses checksum-based change detection — unchanged files are skipped.
+
+### `cognitive_analyze` — Correlate artifacts & reason about knowledge
+
+| Action | Params | Description |
+|--------|--------|-------------|
+| **correlate** | `sourceCollection`, `sourceQuery` or `sourceId`, `targetCollections?`, `minScore?` | Find semantically related artifacts across docs/code/tests. Scores: >0.65 = strong, 0.5–0.65 = partial. |
+| **reason** | `question`, `modules?`, `depth?` (`"shallow"` \| `"deep"`) | Synthesize structured answer with contradiction detection. |
+
+**Examples:**
+```
+cognitive_analyze({ action: "correlate", sourceCollection: "DocumentChunk", sourceQuery: "user authentication" })
+cognitive_analyze({ action: "reason", question: "What are the cross-BC isolation rules?" })
+```
 
-### Analysis & Maintenance
+### `cognitive_admin` — Maintenance & infrastructure
 
-| Tool                 | Description                                                                                |
-| -------------------- | ------------------------------------------------------------------------------------------ |
-| `cognitive_reason`   | Synthesize a structured answer from facts — groups by module/type, detects contradictions. |
-| `cognitive_timeline` | Chronological view with date range filtering and daily grouping.                           |
-| `cognitive_stats`    | Quick dashboard: counts by type/module/status, top tags, recent activity.                  |
-| `cognitive_verify`   | Check if file:line citations still exist on disk.                                          |
-| `cognitive_audit`    | Full quality audit: stale facts, broken citations, duplicate candidates.                   |
-| `cognitive_compact`  | Find and merge duplicate facts (preview or execute mode).                                  |
-| `cognitive_health`   | Weaviate infrastructure health: version, nodes, collections, tenants.                      |
+| Action | Params | Description |
+|--------|--------|-------------|
+| **health** | _(none)_ | Weaviate infrastructure check: nodes, collections, tenants. |
+| **stats** | `module?` | Quick dashboard: counts by type/module/status, top tags, activity. |
+| **audit** | _(none)_ | Deep quality scan: stale facts, broken citations, duplicates, health score. |
+| **compact** | `mode` (`"preview"` \| `"execute"`), `idA?`, `idB?` | Find & merge duplicate facts. Preview first, then execute. |
+| **verify** | `id?` | Check citation integrity (files still exist on disk). Omit `id` to verify all. |
+| **timeline** | `since?`, `until?`, `module?`, `types?`, `status?`, `order?` | Chronological fact view with date filtering and daily grouping. |
 
 ---
 
@@ -248,7 +290,7 @@ cd weaviate-dev-stack
 ./scripts/create-tenant.sh test-isolation-b
 
 # Run tests (uses TEST_TENANT constants, never touches production data)
-pnpm test                  # 162 tests covering all 18 tools + Phase 8 features
+pnpm test                  # 162 tests covering all 5 unified tools + collections
 ```
 
 **Test Coverage:**
@@ -280,7 +322,7 @@ pnpm test                  # 162 tests covering all 18 tools + Phase 8 features
 ┌──────────────────────────────────────────────┐
 │  MCP Protocol (stdio)                        │
 ├──────────────────────────────────────────────┤
-│  server.ts  — auto-registers 18 tools        │
+│  server.ts  — auto-registers 5 tools          │
 ├──────────────────────────────────────────────┤
 │  tools/*.tool.ts  — Zod schema + execute fn  │
 ├──────────────────────────────────────────────┤
@@ -334,7 +376,7 @@ your-project/
 ├── .vscode/
 │   └── mcp.json             # MCP server config (from config/mcp.jsonc)
 ├── .env                     # Environment variables (from config/.env.example)
-└── .gitignore               # Add: .cognitive/pending-facts.json, .cognitive/facts.sqlite
+└── .gitignore               # Add: .cognitive/pending-facts.json
 ```
 
 See [`examples/`](examples/) for pattern & profile templates with detailed documentation.

package/dist/adapters/weaviate-v3.adapter.d.ts.map

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package/dist/adapters/weaviate-v3.adapter.js

@@ -5,6 +5,7 @@ import { getAgentProfile } from '../profiles/agent-profiles.js';
 import { checkCitations, overallCitationStatus } from '../utils/citation-checker.js';
 import { checkDecayBatch } from '../utils/decay.js';
 import { guardReset, guardArchive, guardCompact } from '../utils/safety-guard.js';
+import { computeChecksum } from '../utils/sync-engine.js';
 // ─── Collection Names ───────────────────────────────────────────────────────
 const FACT_COLLECTION = 'CognitiveFact';
 const DOC_COLLECTION = 'DocumentChunk';
@@ -1361,6 +1362,8 @@ export class WeaviateV3Store {
         'lastSynced',
     ];
     async storeDocument(input) {
+        // Auto-calculate checksum if not provided by caller
+        const checksum = input.checksum ?? computeChecksum(input.content);
         // Section included in UUID because a single file can produce multiple chunks (H2 splitting)
         const idSource = input.section
             ? `${input.filePath}:${input.project}:${input.section}`
@@ -1369,13 +1372,13 @@ export class WeaviateV3Store {
             collectionName: DOC_COLLECTION,
             deterministicId: generateUuid5(idSource, 'document'),
             returnProperties: WeaviateV3Store.DOC_RETURN_PROPS,
-            checksum: input.checksum,
+            checksum,
             mutableProperties: {
                 content: input.content,
                 docType: input.docType,
                 module: input.module ?? '',
                 section: input.section ?? '',
-                checksum: input.checksum,
+                checksum,
             },
             identityProperties: {
                 filePath: input.filePath,
@@ -1390,7 +1393,7 @@ export class WeaviateV3Store {
                 project: input.project,
                 module: input.module,
                 section: input.section,
-                checksum: input.checksum,
+                checksum,
                 lastSynced: now,
             }),
         });