kontexta-mcp 2.0.4 → 2.0.5

package/README.md

@@ -3,7 +3,7 @@
 [![npm](https://img.shields.io/npm/v/kontexta-mcp.svg)](https://www.npmjs.com/package/kontexta-mcp)
 [![License: Apache-2.0](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](LICENSE)
 
-MCP server for [Kontexta](https://github.com/safiyu/kontexta) — 46 tools that let agents search, read, edit (section-level), tag, version, and clip web content into a local SQLite-backed knowledge base. Designed for context-window economy: every file-returning response is annotated with `est_tokens` and `size_bytes`.
+MCP server for [Kontexta](https://kontexta.dev) — **53 tools** that let AI coding agents search, read, edit (section-level), tag, version, clip web content, and run sandboxed commands through a local SQLite-backed knowledge base. Designed for context-window economy: every file-returning response is annotated with `est_tokens` and `size_bytes`.
 
 ## Install
 
@@ -25,15 +25,28 @@ The server is launched on demand by your AI client; no global install needed.
 
 `KONTEXTA_DATA_DIR` **must** be an absolute path. The directory is created on first run and holds your SQLite DB plus the markdown files the agent indexes.
 
+### Bin aliases
+
+The package exposes two CLI entry points:
+
+| Command | Description |
+|---|---|
+| `kontexta-mcp` | Standard MCP server entry |
+| `kxta` | Shorthand alias (same binary) |
+
+Both invoke the same `dist/index.js` — use whichever your client's config format prefers.
+
 ## Client config locations
 
 | Client | Path |
 |---|---|
+| Claude Code | `claude mcp add kontexta -s user -e KONTEXTA_DATA_DIR=/path -- node /path/to/apps/mcp/dist/index.js` |
 | Claude Desktop (macOS) | `~/Library/Application Support/Claude/claude_desktop_config.json` |
 | Claude Desktop (Windows) | `%APPDATA%\Claude\claude_desktop_config.json` |
 | Cursor | Settings → Features → MCP |
 | Continue | `~/.continue/config.json` |
 | Codex | `.codex/mcp_servers.json` |
+| GitHub Copilot | File-based (`.github/copilot-instructions.md`) — no MCP config needed |
 | Gemini / Antigravity | `~/.gemini/antigravity/mcp_servers.json` |
 
 ## Web UI (optional)
@@ -46,6 +59,171 @@ docker run -d -p 3000:3000 -v /absolute/path/to/your/data:/app/data safiyu/konte
 
 Open `http://localhost:3000`.
 
+## Tool categories
+
+The 53 tools are organized into these groups:
+
+### Find
+
+| Tool | Purpose |
+|---|---|
+| `search` | Natural-language keyword search across the knowledge base (FTS5) |
+| `regex_search` | Substring/regex search across all indexed files |
+| `grep_in_file` | Substring/regex search within a single known file |
+| `bundle_search` | Search hits + file bodies in a single token-budgeted call |
+| `find_related` | Discover sibling files via tag overlap |
+| `suggest_tags` | Propose tags for an existing file |
+
+### Read
+
+| Tool | Purpose |
+|---|---|
+| `read_file` | Read one file's full body and metadata by ID |
+| `read_files` | Batch read up to 200 files by ID in one call |
+| `read_file_by_path` | Read a file by absolute path (no ID needed) |
+| `read_file_lines` | Read a specific line range from a file |
+| `read_section` | Read a section by heading within a file |
+| `read_file_outline` | Get a compact outline of a file's structure |
+| `describe_file` | Metadata-only inspection (tags, size, history, related) — no body tokens |
+
+### Write
+
+| Tool | Purpose |
+|---|---|
+| `create_file` | Create a new markdown or mermaid file in the KB or project |
+| `create_files` | Create multiple new files in one call |
+| `update_file` | Replace the entire body of a file |
+| `update_file_section` | Surgical edit at a known heading |
+| `delete_file` | Delete a single file |
+| `delete_files` | Delete multiple files in one call |
+| `move_file` | Rename or relocate a file |
+
+### Organize
+
+| Tool | Purpose |
+|---|---|
+| `add_tags` | Add tags to an existing file |
+| `remove_tags` | Remove tags from a file |
+| `list_tags` | Enumerate all tags in the vault |
+| `set_favorite` | Pin / unpin a file |
+| `tag_search_results` | Bulk-tag every hit from a search |
+| `list_folders` | Enumerate folders in a project |
+| `create_folder` | Create a new (possibly nested) folder |
+| `delete_folder` | Remove an empty folder |
+| `list_files` | List files in a project (filterable) |
+
+### History & Recovery
+
+| Tool | Purpose |
+|---|---|
+| `get_history` | List a file's revisions |
+| `get_diff` | Compare two specific revisions |
+| `restore_file` | Roll back a KB file to an earlier revision |
+| `diff_against_disk` | Detect drift after out-of-band filesystem edits |
+| `refresh_index` | Rescan the vault after external changes |
+
+### Discover
+
+| Tool | Purpose |
+|---|---|
+| `list_projects` | Enumerate registered projects |
+| `register_project` | Register a new project root with kontexta |
+| `project_map` | Compact folder/file tree with titles and tags |
+| `stats` | Counts and health metrics for a project |
+| `whats_new` | Files added/changed since a cutoff timestamp |
+
+### Journaling
+
+| Tool | Purpose |
+|---|---|
+| `journal_note` | Record a free-form decision/abandonment/observation note |
+| `journal_intent` | Record a topic/intent pivot |
+| `journal_status` | Report journal backlog and high-water mark |
+| `distill_journal` | Run the distillation pipeline (raw events → markdown summaries) |
+| `distill_journal_commit_upgrades` | Mark mechanical entries as upgraded after subagent dispatch |
+| `housekeep_journal` | Run journal retention/archival (prune old raw files, archive cold tasks) |
+
+### Hands (sandboxed commands)
+
+| Tool | Purpose |
+|---|---|
+| `list_hands` | List every Hands command tool currently registered |
+| `reload_hands` | Re-scan projects and rebuild the Hands tool registry |
+| `confirm_hand` | Approve a pending Hands invocation by its approval token |
+| `describe_hands_schema` | Return the complete `kontexta.json` authoring reference |
+
+### Onboarding
+
+| Tool | Purpose |
+|---|---|
+| `onboard_agent` | Write/update kontexta workflow rules in agent context files |
+| `clip_url` | Clip a web URL into the knowledge base |
+| `commit_backup` | Push KB changes to the project's remote git |
+
+## MCP Resources
+
+The server also exposes two MCP resources for URI-based access:
+
+| URI | Description |
+|---|---|
+| `kontexta://projects` | JSON list of all registered projects with agent-rules status |
+| `kontexta://files/{id}` | Markdown content of a specific file by ID |
+
+## Journaling modes
+
+Kontexta's journaling subsystem has three modes, configurable per project in `kontexta.json`:
+
+| Mode | Behavior |
+|---|---|
+| `lenient` (default) | Never blocks; injects a `journal` envelope on tool responses when backlog exists; auto-distills at 500 events or 7 days |
+| `strict` | Blocks read tools (`search`, `read_*`, `list_*`, `describe_*`) with a `JOURNAL_BACKLOG` error when undistilled events exist. Override with `journal_bypass: true` |
+| `mechanical-only` | Disables LLM-upgrade tier guidance; mechanical distillation runs every N tool calls in-process |
+
+## Hands — sandboxed command orchestration
+
+Hands lets you declare project-specific commands in `kontexta.json` that agents can run safely:
+
+- **Strict sandbox**: realpath-verified CWD, stripped `PATH`, clean environment, ring-buffer output cap, hard timeouts, process-group kill on timeout, no shell.
+- **Cryptographic confirm tokens** (CSPRNG, single-use, 60s expiry) for high-risk commands.
+- **ReDoS-proof parameter validation** via `re2`; default `^[^-].*` mitigates argv injection.
+- **Human-in-the-loop**: Optional approval flow per command.
+
+## Token-aware responses
+
+Every file-returning tool annotates its response with:
+
+- `size_bytes` — exact byte size of the content
+- `est_tokens` — estimated token count (≈1 token per 4 ASCII chars)
+
+This lets agents budget their context window before deciding to fetch more files. A token budget warning is emitted when a project's content exceeds the soft cap (default 100,000 tokens).
+
+## Agent rules
+
+Kontexta injects a version-stamped workflow rules block into agent context files (`CLAUDE.md`, `AGENTS.md`, `.cursor/rules/*.mdc`, `.github/copilot-instructions.md`, etc.) via `onboard_agent`. The server checks for outdated rules on every tool call and surfaces a warning when a newer `rulesVersion` is available.
+
+Supported agents: Claude Code, Cursor, Cline, GitHub Copilot, Gemini, Antigravity, Continue, Cline.
+
+## Graceful shutdown
+
+The MCP server drains in-flight work on `SIGINT`/`SIGTERM`:
+
+1. Kills detached Hands children
+2. Flushes the journal capture
+3. Awaits in-flight database operations (up to 10s hard ceiling)
+4. Closes the database cleanly
+
+## Environment variables
+
+| Variable | Default | Description |
+|---|---|---|
+| `KONTEXTA_DATA_DIR` | `~/.local/share/kontexta` (Linux) | Vault directory (SQLite DB + markdown files) |
+| `KONTEXTA_DB_PATH` | `$KONTEXTA_DATA_DIR/kontexta.db` | Override the database file path |
+| `KONTEXTA_DEFAULT_PROJECT_SLUG` | `"default"` | Default project for journal capture |
+| `KONTEXTA_AGENT` | `"unknown"` | Agent identifier for journal events |
+| `KONTEXTA_PROJECT_PATH` | `process.cwd()` | Project path for git polling |
+| `KONTEXTA_PROJECT_TOKEN_WARN` | `100000` | Token budget soft cap warning threshold |
+| `KONTEXTA_PROJECTS` | — | Colon-separated list of project directories to auto-register |
+
 ## Requirements
 
 - Node ≥ 20 (the package is published as ESM, target node20).
@@ -53,7 +231,7 @@ Open `http://localhost:3000`.
 
 ## Documentation
 
-Full docs, the reference for 46 core + unlimited custom hand tools, and the web UI live in the [main repository](https://github.com/safiyu/kontexta). See [`CHANGELOG.md`](https://github.com/safiyu/kontexta/blob/main/CHANGELOG.md) for what's new.
+Full docs, the complete tool reference with routing matrices, and the web UI live in the [main repository](https://github.com/safiyu/kontexta). See [`CHANGELOG.md`](https://github.com/safiyu/kontexta/blob/main/CHANGELOG.md) for what's new and [`docs/MCP.md`](https://github.com/safiyu/kontexta/blob/main/docs/MCP.md) for the detailed MCP integration guide.
 
 ## License
 

package/dist/index.js

@@ -277,9 +277,13 @@ import { join as join2, dirname } from "path";
 import { fileURLToPath } from "url";
 function resolveMigrationsDir() {
   const candidates = [
+    // Docker: WORKDIR=/app, migrations explicitly copied to /app/packages/core/src/db/migrations
+    join2(process.cwd(), "packages", "core", "src", "db", "migrations"),
+    // tsc build: dist/db/migrations (sibling of this file's dist location)
     join2(__dirname2, "migrations"),
+    // Next.js standalone: __dirname resolves relative to the traced module
     join2(__dirname2, "..", "..", "src", "db", "migrations"),
-    join2(process.cwd(), "packages", "core", "src", "db", "migrations"),
+    // Fallback: dist copy
     join2(process.cwd(), "packages", "core", "dist", "db", "migrations"),
     join2(process.cwd(), "..", "..", "packages", "core", "src", "db", "migrations"),
     join2(process.cwd(), "..", "..", "packages", "core", "dist", "db", "migrations")

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "kontexta-mcp",
-  "version": "2.0.4",
+  "version": "2.0.5",
   "description": "The local Brain and Hands for AI coding agents (MCP Server)",
   "keywords": [
     "mcp",