Add session documentation system (migration + MCP tools)

Phase 1-2 complete: Database schema + 9 MCP tools for session docs

Database Changes (migration 016):
- session_notes table (accomplishments, decisions, gotchas, etc.)
- session_plans table (plan mode plans with lifecycle tracking)
- project_documentation table (persistent project docs)
- sessions.documentation column (auto-generated markdown)
- HNSW indexes for semantic search across all doc types

MCP Tools Added (session-docs.ts):
1. session_note_add - Add structured notes to session
2. session_notes_list - List notes by type
3. session_plan_save - Save plan with embedding
4. session_plan_update_status - Track plan lifecycle
5. session_plan_list - List session plans
6. project_doc_upsert - Create/update project docs
7. project_doc_get - Get specific doc by type
8. project_doc_list - List all project docs
9. session_documentation_generate - Auto-generate markdown

Replaces: CLAUDE.md files, ~/.claude/plans/ directory

Next: Update session-start/end scripts for temp file management

Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>

src/index.ts

@@ -49,6 +49,17 @@ import {
   buildRecord,
   sessionCommitLink,
 } from './tools/sessions.js';
+import {
+  sessionNoteAdd,
+  sessionNotesList,
+  sessionPlanSave,
+  sessionPlanUpdateStatus,
+  sessionPlanList,
+  projectDocUpsert,
+  projectDocGet,
+  projectDocList,
+  sessionDocumentationGenerate,
+} from './tools/session-docs.js';
 
 // Create MCP server
 const server = new Server(
@@ -476,6 +487,82 @@ server.setRequestHandler(CallToolRequestSchema, async (request) => {
         );
         break;
 
+      // Session Documentation
+      case 'session_note_add':
+        result = await sessionNoteAdd({
+          session_id: a.session_id,
+          note_type: a.note_type,
+          content: a.content,
+        });
+        break;
+      case 'session_notes_list':
+        result = JSON.stringify(
+          await sessionNotesList({
+            session_id: a.session_id,
+            note_type: a.note_type,
+          }),
+          null,
+          2
+        );
+        break;
+      case 'session_plan_save':
+        result = await sessionPlanSave({
+          session_id: a.session_id,
+          plan_content: a.plan_content,
+          plan_file_name: a.plan_file_name,
+          status: a.status,
+        });
+        break;
+      case 'session_plan_update_status':
+        result = await sessionPlanUpdateStatus({
+          plan_id: a.plan_id,
+          status: a.status,
+        });
+        break;
+      case 'session_plan_list':
+        result = JSON.stringify(
+          await sessionPlanList({
+            session_id: a.session_id,
+            status: a.status,
+          }),
+          null,
+          2
+        );
+        break;
+      case 'project_doc_upsert':
+        result = await projectDocUpsert({
+          project: a.project,
+          doc_type: a.doc_type,
+          title: a.title,
+          content: a.content,
+          session_id: a.session_id,
+        });
+        break;
+      case 'project_doc_get':
+        result = JSON.stringify(
+          await projectDocGet({
+            project: a.project,
+            doc_type: a.doc_type,
+          }),
+          null,
+          2
+        );
+        break;
+      case 'project_doc_list':
+        result = JSON.stringify(
+          await projectDocList({
+            project: a.project,
+          }),
+          null,
+          2
+        );
+        break;
+      case 'session_documentation_generate':
+        result = await sessionDocumentationGenerate({
+          session_id: a.session_id,
+        });
+        break;
+
       default:
         throw new Error(`Unknown tool: ${name}`);
     }