docs: update wiki references to WikiManager, fix test counts

docs/00-index.md

@@ -52,11 +52,11 @@ python -m mcp_server --transport stdio
 | 05 | [Knowledge Graph](05-graph.md) | EpistemicGraph, TemporalGraph |
 | 06 | [Lifecycle](06-lifecycle.md) | Type-aware Forgetting, EmotionTrigger, Consolidation, Importance Scheduler |
 | 07 | [Hooks](07-hooks.md) | 24 hooks (12 user + 12 agent), type-aware gating |
-| 08 | [Wiki](08-wiki.md) | FileWiki (.md files + FTS5), 14 types |
+| 08 | [Wiki](08-wiki.md) | WikiManager (.md files + FTS5), 14 types |
 | 09 | [Features](09-features.md) | Auth, Backup, Dashboard, Audit, RateLimit, Secrets |
 | 10 | [Shared](10-shared.md) | Saga+Retry+Idempotency, Importance Scorer, Middleware, Embeddings |
 | 11 | [Operations](11-operations.md) | Transports, Health, Auth, Scheduler, Configuration |
-| 12 | [Testing](12-testing.md) | pytest (338 tests + 25 Hypothesis), benchmarks, project structure |
+| 12 | [Testing](12-testing.md) | pytest (372 tests + 25 Hypothesis), benchmarks, project structure |
 
 ---
 
@@ -87,7 +87,7 @@ python -m mcp_server --transport http --port 8000
 
 - **Version:** 1.0.0
 - **MCP Tools:** 19
-- **Tests:** 338 passed (25 property-based Hypothesis)
+- **Tests:** 372 passed (25 property-based Hypothesis)
 - **Python files:** 70
 - **DB tables:** 23
 - **Hooks:** 24

docs/01-architecture.md

@@ -79,9 +79,9 @@ Message → L1 (buffer)
 | `epi_tags` | graph/epistemic.py | Epistemic node tags (fast JOIN lookup) |
 | `temporal_events` | graph/temporal.py | Temporal events |
 | `temporal_links` | graph/temporal.py | Temporal links |
-| `user_wiki` | wiki/user_wiki.py | User wiki entries |
-| `agent_wiki` | wiki/agent_wiki.py | Agent wiki entries |
-| `wiki_index` | wiki/file_wiki.py | Wiki FTS5 index |
+| `user_wiki` | wiki/manager.py | User wiki entries |
+| `agent_wiki` | wiki/manager.py | Agent wiki entries |
+| `wiki_index` | wiki/manager.py | Wiki FTS5 index |
 | `memory_conflicts` | rag/conflict.py | Memory conflicts |
 | `memory_kind_registry` | shared/memory_types.py | Typed memory categories |
 | `importance_audit` | lifecycle/importance_scheduler.py | Importance rescore audit log |

docs/04-rag.md

@@ -564,7 +564,7 @@ chunks = rag._chunk_text("A" * 1000, max_size=500, overlap=100)
 ### Constructor
 
 ```python
-MultiSourceRAG(rag: RAGEngine, wiki: FileWiki, cm: AsyncConnectionManager = None)
+MultiSourceRAG(rag: RAGEngine, wiki: WikiManager, cm: AsyncConnectionManager = None)
 ```
 
 ### `search()`
@@ -597,9 +597,9 @@ The MCP tool `memory_search_rrf` uses MultiSourceRAG under the hood when `source
 ```python
 from rag.multi_source import MultiSourceRAG
 from rag.engine import RAGEngine
-from wiki.file_wiki import FileWiki
+from wiki.manager import WikiManager
 
-ms = MultiSourceRAG(rag=RAGEngine(layer="user"), wiki=FileWiki(layer="user"))
+ms = MultiSourceRAG(rag=RAGEngine(layer="user"), wiki=WikiManager(layer="user"))
 results = await ms.search("memory architecture", user_id="alice", limit=5)
 # Merged + deduplicated results from RAG and Wiki
 ```

docs/08-wiki.md

@@ -1,8 +1,8 @@
-# Wiki — wiki/ (FileWiki + UserWiki/AgentWiki with FTS5)
+# Wiki — wiki/ (WikiManager with FTS5)
 
 ## Shared Utilities (wiki/shared.py)
 
-Common wiki logic extracted from agent_wiki.py, file_wiki.py, user_wiki.py:
+Common wiki logic:
 
 | Function | Purpose |
 |----------|---------|
@@ -15,9 +15,10 @@ Common wiki logic extracted from agent_wiki.py, file_wiki.py, user_wiki.py:
 | `build_count_query(table, user_id, wiki_type)` | COUNT query builder |
 | `format_search_result(row)` | FTS result formatter |
 
-## FileWiki (`wiki/file_wiki.py`) — core module
+## WikiManager (`wiki/manager.py`) — unified module
 
-.md files = source of truth + SQLite FTS5 index.
+Layer-based wiki: .md files = source of truth + SQLite FTS5 index.
+Replaces former FileWiki, UserWiki, AgentWiki classes.
 
 ### FTS5 content-sync table
 
@@ -65,11 +66,11 @@ wiki:
     external_dirs: ["/home/user/notes"]
 ```
 
-### FileWiki Methods
+### WikiManager Methods
 
 ```python
-from wiki.file_wiki import FileWiki
-uw = FileWiki(layer="user")
+from wiki.manager import WikiManager
+uw = WikiManager(layer="user")
 
 # add() — creates .md + indexes (skips on MD5 match)
 await uw.add("diary", "Day 1", "Content", tags=["work"])
@@ -84,7 +85,7 @@ await uw.reindex_all()
 await uw.sync_external(["/home/user/notes"])
 ```
 
-## UserWiki (`wiki/user_wiki.py`) — 7 types, 590 lines
+## UserWiki (layer=user) (deprecated - use WikiManager) (`wiki/manager.py`) — 7 types, 590 lines
 
 Legacy module for user wiki with FTS5. Each type is a separate category.
 
@@ -99,14 +100,14 @@ Legacy module for user wiki with FTS5. Each type is a separate category.
 | `retrospective` | Retrospective |
 
 ```python
-from wiki.user_wiki import UserWiki
-uw = UserWiki()
+from wiki.manager import WikiManager
+uw = WikiManager(layer='user')
 await uw.add("diary", "Day 1", "Started project", ["work"], 0.7)
 results = await uw.search("project")  # FTS5 search
 await uw.sync_external(["/home/user/notes"])  # import .md
 ```
 
-### UserWiki — All public methods
+### UserWiki (layer=user) (deprecated - use WikiManager) — All public methods
 
 | Method | Signature | Returns | Async |
 |--------|-----------|---------|-------|
@@ -124,7 +125,7 @@ await uw.sync_external(["/home/user/notes"])  # import .md
 
 **WikiEntry dataclass:** `entry_id: int, user_id: str, wiki_type: str, title: str, content: str, tags: List[str], importance: float, created_at: float, updated_at: float`
 
-## AgentWiki (`wiki/agent_wiki.py`) — 7 types, 590 lines
+## AgentWiki (layer=agent) (deprecated - use WikiManager) (`wiki/manager.py`) — 7 types, 590 lines
 
 Legacy module for agent wiki. Lore, references, decision journal.
 
@@ -139,14 +140,14 @@ Legacy module for agent wiki. Lore, references, decision journal.
 | `principle_log` | Principle journal |
 
 ```python
-from wiki.agent_wiki import AgentWiki
-aw = AgentWiki()
+from wiki.manager import WikiManager
+aw = WikiManager(layer='agent')
 await aw.add("decision_log", "DB Choice", "SQLite for simplicity", ["tech"], 0.8)
 results = await aw.search("SQLite")
 await aw.sync_external(["/path/to/lore"])
 ```
 
-### AgentWiki — All public methods
+### AgentWiki (layer=agent) (deprecated - use WikiManager) — All public methods
 
 | Method | Signature | Returns | Async |
 |--------|-----------|---------|-------|
@@ -225,13 +226,13 @@ updated: 2026-06-21T22:00:00
 Discussed the plan for the week.
 ```
 
-## FileWiki Methods (async)
+## WikiManager Methods (async)
 
 ```python
-from wiki.file_wiki import FileWiki
+from wiki.manager import WikiManager
 
-uw = FileWiki(layer="user")
-aw = FileWiki(layer="agent")
+uw = WikiManager(layer="user")
+aw = WikiManager(layer="agent")
 
 # Write
 path = await uw.add("diary", "Day 1", "Started project", tags=["work"], importance=0.7)
@@ -259,7 +260,7 @@ await uw.reindex_all()
 await uw.sync_external(["/home/user/notes"])
 ```
 
-### FileWiki — All public methods
+### WikiManager — All public methods
 
 | Method | Signature | Returns | Async |
 |--------|-----------|---------|-------|

docs/12-testing.md

@@ -125,7 +125,7 @@ mcp-ariel-memory/
 ├── graph/                     # Epistemic + Temporal (async)
 ├── lifecycle/                 # Forgetting + Emotion + Consolidation (async)
 ├── hooks/                     # 24 hooks
-├── wiki/                      # FileWiki (.md + FTS5, async)
+├── wiki/                      # WikiManager (.md + FTS5, async)
 ├── features/                  # Auth + Backup + Dashboard + Audit + RateLimit + Secrets (async)
 └── shared/                    # ConnectionManager + Cache + Saga + Middleware + Embeddings (async)
 ```

docs/changelog.md

@@ -19,7 +19,7 @@
 - Health endpoints
 
 ### Testing
-- 338 tests passing
+- 372 tests passing
 - 25 property-based Hypothesis tests
 - CI on Python 3.10-3.13
 - Type checking (mypy)

docs/index.md

@@ -3,7 +3,7 @@
 **Universal Two-Layer Memory MCP Server for AI agents**
 
 [![CI](https://github.com/Cipher208/mcp-ariel-memory/actions/workflows/ci.yml/badge.svg)](https://github.com/Cipher208/mcp-ariel-memory/actions/workflows/ci.yml)
-[![Tests](https://img.shields.io/badge/tests-338 passed-brightgreen)](https://github.com/Cipher208/mcp-ariel-memory/actions)
+[![Tests](https://img.shields.io/badge/tests-372 passed-brightgreen)](https://github.com/Cipher208/mcp-ariel-memory/actions)
 [![Python](https://img.shields.io/badge/python-3.10--3.13-blue)](https://www.python.org/)
 
 ---
@@ -78,7 +78,7 @@ mcp-ariel-memory is a production-ready MCP server providing persistent, searchab
 ## Status
 
 - **Version:** 1.0.0
-- **Tests:** 338 passed (including 25 property-based Hypothesis tests)
+- **Tests:** 372 passed (including 25 property-based Hypothesis tests)
 - **DB tables:** 23
 - **Python:** 3.10–3.13
 - **Platform:** Windows, Linux, macOS, Docker

docs/wiki/agent-wiki.md

@@ -1,13 +1,13 @@
-# AgentWiki
+# AgentWiki (deprecated - use WikiManager)
 
 Agent identity wiki for storing agent learning and evolution.
 
 ## Usage
 
 ```python
-from wiki.agent_wiki import AgentWiki
+from wiki.manager import WikiManager
 
-aw = AgentWiki()
+aw = WikiManager(layer='agent')
 
 # Add page
 await aw.add_page(

docs/wiki/file-wiki.md

@@ -1,4 +1,4 @@
-# FileWiki
+# WikiManager
 
 File-based wiki with .md files as source of truth.
 
@@ -12,9 +12,9 @@ File-based wiki with .md files as source of truth.
 ## Usage
 
 ```python
-from wiki.file_wiki import FileWiki
+from wiki.manager import WikiManager
 
-fw = FileWiki(layer="user")
+fw = WikiManager(layer="user")
 
 # Add page
 fw.add_page(

docs/wiki/overview.md

@@ -8,36 +8,36 @@ Wiki system with .md files as source of truth and FTS5 full-text search.
 
 14 types: spec, decision, error, code, note, guide, reference, tutorial, faq, changelog, architecture, api, example, concept
 
-## FileWiki
+## WikiManager
 
 File-based wiki with external folder sync:
 
 ```python
-from wiki.file_wiki import FileWiki
+from wiki.manager import WikiManager
 
-fw = FileWiki(layer="user")
+fw = WikiManager(layer="user")
 fw.add_page(title="Architecture", content="# Architecture\n...", wiki_type="spec")
 results = fw.search("architecture", limit=5)
 ```
 
-## UserWiki
+## UserWiki (layer=user) (deprecated - use WikiManager)
 
 User-specific wiki pages:
 
 ```python
-from wiki.user_wiki import UserWiki
+from wiki.manager import WikiManager
 
-uw = UserWiki()
+uw = WikiManager(layer='user')
 await uw.add_page(user_id="u1", title="My Notes", content="...")
 ```
 
-## AgentWiki
+## AgentWiki (layer=agent) (deprecated - use WikiManager)
 
 Agent identity wiki:
 
 ```python
-from wiki.agent_wiki import AgentWiki
+from wiki.manager import WikiManager
 
-aw = AgentWiki()
+aw = WikiManager(layer='agent')
 await aw.add_page(title="Learning", content="...")
 ```

docs/wiki/user-wiki.md

@@ -1,13 +1,13 @@
-# UserWiki
+# UserWiki (deprecated - use WikiManager)
 
 User-specific wiki pages stored in database.
 
 ## Usage
 
 ```python
-from wiki.user_wiki import UserWiki
+from wiki.manager import WikiManager
 
-uw = UserWiki()
+uw = WikiManager(layer='user')
 
 # Add page
 await uw.add_page(