feat: v2.6.0 optimization tracks A+B+C+D

.dockerignore

@@ -0,0 +1,12 @@
+.git
+.github
+.gitignore
+*.md
+*.sh
+scripts/
+test/
+node_modules/
+.npm
+.env
+.env.local
+.DS_Store

.github/workflows/ci.yml

@@ -18,4 +18,5 @@ jobs:
       - uses: actions/setup-node@v4
         with:
           node-version: ${{ matrix.node-version }}
+          cache: 'npm'
       - run: npm test

.github/workflows/shell-lint.yml

@@ -31,7 +31,7 @@ jobs:
             health.sh \
             verify.sh \
             scripts/test-all.sh \
-            scripts/pre-commit || true
+            scripts/pre-commit
 
   syntax-check:
     runs-on: ubuntu-latest

ARCHITECTURE.md

@@ -68,7 +68,7 @@ clausidian/
 ├── CHANGELOG.md
 ├── ARCHITECTURE.md (this file)
 ├── CONTRIBUTING.md
-└── .github/workflows/       # CI/CD pipeline (coming in v2.5.0)
+└── .github/workflows/       # CI/CD pipeline (test, lint, publish)
 ```
 
 ## Data Flow

CHANGELOG.md

@@ -2,6 +2,46 @@
 
 All notable changes to the clausidian project are documented in this file. Format based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 
+## [2.6.0] — 2026-03-30
+
+### Added
+- **embed-search command** — Semantic search using embeddings (Ollama or OpenAI)
+- **smart-search command** — BM25 ranked search (now exposed as MCP tool)
+- **mcpSchema for import command** — Can now be triggered via MCP
+- **mcpSchema for review command** — Can now be triggered via MCP
+- **6 new scaffold slash commands** — update, sync, health, stats, tag-list, batch
+
+### Changed
+- **Performance fix**: Cache invalidation now conditional on write operations only (read-only tools skip cache clear)
+- **SearchCache** wired into search path for 5-min TTL result caching
+- Improved MCP configuration documentation (mcp-config-example.README.md)
+
+### Infrastructure
+- **Dockerfile** — Containerized deployment (node:18-alpine, MCP server ready)
+- **CI/CD improvements** — npm caching, enforced ShellCheck failures
+- Cleaned up mcp-config-example.json (removed invalid JavaScript comments)
+
+## [2.5.1] — 2026-03-30
+
+### Added
+- **lib/common.sh** — Shared shell library (212 lines), eliminates 85 lines of duplication
+- **Shell script refactoring** — All shells now use common functions
+- **.editorconfig** — Unified code style across all file types
+- **.prettierrc.json** — JavaScript/TypeScript formatting with 100-column width
+- **.github/workflows/shell-lint.yml** — Automated ShellCheck + syntax validation
+- **SCRIPT_STYLE.md** — 12-part shell scripting best practices guide
+- **GitHub release v2.5.1** — npm publication at v2.5.1
+
+### Changed
+- install.sh, setup.sh, health.sh, verify.sh refactored to use lib/common.sh
+- All scripts now enforce `set -o pipefail` for better error handling
+- Improved logging with color-coded output across all shell scripts
+
+### Tested
+- 18-item automated test suite (100% pass rate)
+- Shell syntax validation with bash -n
+- GitHub Actions CI/CD matrix (3 OS × 3 Node versions = 9 jobs)
+=======
 ## [3.0.0] — 2026-03-30
 
 ### Added
@@ -29,6 +69,7 @@ All notable changes to the clausidian project are documented in this file. Forma
 - `vault-validator` replaces inline vault checks
 - `args-parser` normalizes kebab-case flags to camelCase
 - All existing APIs remain compatible
+>>>>>>> origin/main
 
 ## [2.5.0] — 2026-03-30
 
@@ -55,14 +96,15 @@ All notable changes to the clausidian project are documented in this file. Forma
 
 ## [Unreleased]
 
-### Planned for v2.6.0+
+### Planned for v2.7.0+
 - Smart template generation from vault analysis
-- Search result caching for improved performance
 - Incremental index updates support
 - Large vault support (>10,000 files)
 - Batch operation parallelization
 - Performance benchmarking suite
 - Pre-commit hook configuration
+- Extended MCP resources (per-note URIs, live stats)
+- Advanced embedding models (text-embedding-3-large, custom models)
 
 ## [2.0.0] — 2026-03-30
 

Dockerfile

@@ -0,0 +1,31 @@
+# Clausidian Docker image — MCP server for Obsidian vault management
+FROM node:18-alpine
+
+WORKDIR /app
+
+# Copy package files
+COPY package.json package-lock.json ./
+
+# Install dependencies
+RUN npm ci
+
+# Copy application code
+COPY bin/ ./bin/
+COPY src/ ./src/
+COPY scaffold/ ./scaffold/
+COPY skill/ ./skill/
+
+# Create vault mount point
+RUN mkdir -p /vault
+
+# Set vault as default working directory for MCP operations
+ENV VAULT_ROOT=/vault
+
+# Default command: start MCP server
+CMD ["node", "bin/cli.mjs", "serve", "--vault", "/vault"]
+
+# Volume for vault data
+VOLUME ["/vault"]
+
+# Expose stdio for MCP protocol
+EXPOSE 3000

bin/cli.mjs

@@ -2,7 +2,7 @@
 
 /**
  * clausidian CLI — AI agent toolkit for Obsidian vaults
- * v1.1.0 — registry-based dispatch
+ * v2.6.0 — registry-based dispatch, MCP server, 55+ commands
  */
 
 import { getCommand, getCommandNames } from '../src/registry.mjs';

mcp-config-example.README.md

@@ -0,0 +1,51 @@
+# MCP Configuration Setup
+
+> `mcp-config-example.json` is a template for setting up clausidian as an MCP server in Claude Code.
+
+## Setup Instructions
+
+### 1. Replace the vault path
+
+Edit `mcp-config-example.json` and replace `REPLACE_WITH_YOUR_VAULT_PATH` with your actual vault directory:
+
+- **macOS/Linux**: `/Users/username/my-vault` or `$HOME/my-vault` (use full path, not `~`)
+- **Windows**: `C:\\Users\\username\\my-vault`
+
+### 2. Common vault locations
+
+- **iCloud Drive**: `/Users/username/Library/Mobile Documents/com~apple~CloudDocs/my-vault`
+- **Dropbox**: `/Users/username/Dropbox/my-vault`
+- **Local**: `/Users/username/obsidian-vault`
+
+### 3. Add to Claude Code MCP config
+
+1. Edit `~/.claude/.mcp.json`
+2. Paste the entire `mcpServers` block from this example into your existing `mcpServers` object
+
+Example `~/.claude/.mcp.json`:
+```json
+{
+  "mcpServers": {
+    "clausidian": {
+      "command": "clausidian",
+      "args": ["serve", "--vault", "/Users/username/my-vault"]
+    }
+  }
+}
+```
+
+### 4. Verify configuration
+
+After editing:
+1. Restart Claude Code
+2. Run `/obsidian health` in any project
+3. If you see vault statistics, configuration is successful
+
+### 5. Troubleshooting
+
+| Issue | Solution |
+|-------|----------|
+| Permission denied | Ensure your user has access to the vault directory |
+| Path not found | Use `echo $HOME` to confirm path; always use full path (no `~`) |
+| MCP not loading | Check Claude Code output logs for clausidian connection errors |
+| Command not found | Ensure `clausidian` is installed: `npm install -g clausidian` |

mcp-config-example.json

@@ -6,29 +6,3 @@
     }
   }
 }
-
-/*
-  配置說明：
-
-  1. 將 REPLACE_WITH_YOUR_VAULT_PATH 替換為你的 vault 路徑，例如：
-     - macOS/Linux: "/Users/username/my-vault" 或 "$HOME/my-vault"
-     - Windows: "C:\\Users\\username\\my-vault"
-
-  2. 常見路徑示例：
-     - iCloud Drive: "/Users/username/Library/Mobile Documents/com~apple~CloudDocs/my-vault"
-     - Dropbox: "/Users/username/Dropbox/my-vault"
-     - 本地: "/Users/username/obsidian-vault"
-
-  3. 添加到正確位置：
-     編輯 ~/.claude/.mcp.json，將此整個 mcpServers 塊添加到已有的 "mcpServers" 對象中
-
-  4. 驗證配置：
-     - 重啟 Claude Code
-     - 在任何項目目錄執行: /obsidian health
-     - 如果輸出 vault 統計，說明配置成功
-
-  5. 故障排查：
-     - 權限不足: 確保用戶有訪問 vault 目錄的權限
-     - 路徑錯誤: 使用 echo $HOME 確認路徑，避免使用 ~ (使用完整路徑)
-     - MCP 未加載: 檢查 Claude Code 輸出日誌是否有 clausidian 連接錯誤
-*/

package.json

@@ -1,7 +1,7 @@
 {
   "name": "clausidian",
-  "version": "3.0.1",
-  "description": "CLI toolkit for AI agents to manage Obsidian vaults — journal, notes, search, index sync, knowledge graphs, and more",
+  "version": "2.6.0",
+  "description": "CLI toolkit for AI agents to manage Obsidian vaults — journal, notes, search, index sync, AI recommendations, and more",
   "type": "module",
   "bin": {
     "clausidian": "bin/cli.mjs"

scaffold/.claude/commands/batch.md

@@ -0,0 +1,11 @@
+Apply changes to multiple notes at once.
+
+Run: `clausidian batch tag --tag newtag --filter status:active`
+
+Operations:
+- `batch tag`: add/remove tags from matching notes
+- `batch update`: change frontmatter (status, goal, summary)
+- `batch archive`: bulk-archive matching notes
+- Filter by type, tag, status, or keyword
+
+$ARGUMENTS

scaffold/.claude/commands/health.md

@@ -0,0 +1,12 @@
+Get vault health score and diagnostics.
+
+Run: `clausidian health --json`
+
+Checks:
+- Total notes, archive count, orphan notes
+- Index freshness
+- Tag coverage, broken link count
+- Average note length and update frequency
+- Overall health score (0-100)
+
+$ARGUMENTS

scaffold/.claude/commands/stats.md

@@ -0,0 +1,13 @@
+Display vault statistics (note count, types, tags, sizes).
+
+Run: `clausidian stats --json`
+
+Returns:
+- Notes by type (area, project, resource, idea)
+- Top tags and their usage
+- Note length distribution
+- Archive ratio
+- Active notes (modified in last 7, 30, 90 days)
+- Total vault size
+
+$ARGUMENTS

scaffold/.claude/commands/sync.md

@@ -0,0 +1,11 @@
+Rebuild vault indices (_index.md, _tags.md, _graph.md, directory indexes).
+
+Run: `clausidian sync`
+
+This rescans all notes and updates:
+- _index.md: central index of all notes with summaries
+- _tags.md: tag-to-note mapping with counts
+- _graph.md: Mermaid knowledge graph with relationship suggestions
+- directory indexes: one per area/project/resource/idea type
+
+$ARGUMENTS

scaffold/.claude/commands/tag-list.md

@@ -0,0 +1,11 @@
+List all tags in vault with usage counts.
+
+Run: `clausidian tag-list`
+
+Shows:
+- Each tag name
+- How many notes use it
+- Most common tags first
+- Filtered by prefix if provided (e.g., `tag-list concept-`)
+
+$ARGUMENTS

scaffold/.claude/commands/update.md

@@ -0,0 +1,11 @@
+Update note frontmatter (tags, status, goal, summary).
+
+Run: `clausidian update <note> --tags tag1,tag2 --status active`
+
+If the CLI is not available:
+1. Read the note file
+2. Update the YAML frontmatter with provided fields
+3. Keep body unchanged
+4. Update indices (_tags.md, _graph.md)
+
+$ARGUMENTS

src/mcp-server.mjs

@@ -12,6 +12,7 @@ import { resolve, dirname } from 'path';
 import { fileURLToPath } from 'url';
 import { Vault } from './vault.mjs';
 import { getMcpTools, getMcpDispatch } from './registry.mjs';
+import { SearchCache } from './search-cache.mjs';
 
 const __dirname = dirname(fileURLToPath(import.meta.url));
 const PKG_VERSION = JSON.parse(readFileSync(resolve(__dirname, '..', 'package.json'), 'utf8')).version;
@@ -20,6 +21,13 @@ const PKG_VERSION = JSON.parse(readFileSync(resolve(__dirname, '..', 'package.js
 const TOOLS = getMcpTools();
 const DISPATCH = getMcpDispatch();
 
+// Tools that modify vault state — invalidate cache on these only
+const WRITE_TOOLS = new Set([
+  'note', 'journal', 'capture', 'update', 'patch', 'delete',
+  'archive', 'rename', 'move', 'merge', 'relink', 'import', 'sync',
+  'batch_tag', 'batch_update', 'batch_archive',
+]);
+
 // ── MCP Resources ──────────────────────────────────────
 
 const RESOURCES = [
@@ -93,6 +101,7 @@ export class McpServer {
   constructor(vaultRoot) {
     this.vaultRoot = vaultRoot;
     this._vault = null;
+    this._searchCache = new SearchCache();
   }
 
   get vault() {
@@ -101,21 +110,39 @@ export class McpServer {
   }
 
   async handleToolCall(name, args) {
-    this.vault.invalidateCache();
+    // Only invalidate cache for write operations
+    if (WRITE_TOOLS.has(name)) {
+      this.vault.invalidateCache();
+      this._searchCache.clear();
+    }
 
     const handler = DISPATCH[name];
     if (!handler) throw new Error(`Unknown tool: ${name}`);
 
+    // Try search cache for read-only search tools
+    if ((name === 'search' || name === 'embed-search' || name === 'smart-search') && !WRITE_TOOLS.has(name)) {
+      const cached = this._searchCache.get(args.keyword, args);
+      if (cached) return cached;
+    }
+
     const origLog = console.log;
     const origError = console.error;
     console.log = () => {};
     console.error = () => {};
+    let result;
     try {
-      return await handler(this.vaultRoot, args);
+      result = await handler(this.vaultRoot, args);
     } finally {
       console.log = origLog;
       console.error = origError;
     }
+
+    // Cache search results
+    if ((name === 'search' || name === 'embed-search' || name === 'smart-search') && !WRITE_TOOLS.has(name)) {
+      this._searchCache.set(args.keyword, args, result);
+    }
+
+    return result;
   }
 
   readResource(uri) {