Ogro-Projukti · FatinShadab · Jun 6, 2026 · Jun 2, 2026 · Jun 5, 2026 · Jun 6, 2026
diff --git a/.cursor/mcp.json b/.cursor/mcp.json
@@ -0,0 +1,10 @@
+{
+  "mcpServers": {
+    "codegenome": {
+      "command": "codegenome",
+      "args": [
+        "mcp-start"
+      ]
+    }
+  }
+}
diff --git a/.cursor/rules/watcher-knowledge-graph.mdc → .cursor/rules/codegenome-knowledge-graph.mdc b/.cursor/rules/watcher-knowledge-graph.mdc → .cursor/rules/codegenome-knowledge-graph.mdc
@@ -9,7 +9,7 @@ You are operating within a repository analyzed by CodeGenome, an architectural k
 
 ## Core Directives
 
-1. **Mandatory MCP Usage**: When `.genome/watcher.db` exists, you MUST use CodeGenome MCP access for all codebase, architecture, dependency, or symbol queries whenever it is available.
+1. **Mandatory MCP Usage**: When `.genome/codegenome.db` exists, you MUST use CodeGenome MCP access for all codebase, architecture, dependency, or symbol queries whenever it is available.
 2. **Access Order**: First use native CodeGenome MCP tools exposed in your context. If those tools are missing, you MAY try a local MCP HTTP endpoint such as `http://127.0.0.1:7331/mcp` when the user has started it or configured it. Treat this as MCP transport access, not as an arbitrary application HTTP API.
 3. **Prefer Graph over Grep**: Use graph-backed MCP tools instead of raw file searching (`grep`) or reading entire files blindly. The graph provides semantic understanding.
 4. **Fallback Gracefully**: If native MCP tools are missing and HTTP MCP access is unavailable, incompatible, or returns empty data, tell the user exactly what failed and what to configure. Then, if needed, read `.genome/graph.json` or `.genome/exports/*.md` before resorting to standard text searches.

diff --git a/.github/copilot-instructions.md b/.github/copilot-instructions.md
@@ -4,7 +4,7 @@ You are operating within a repository analyzed by CodeGenome, an architectural k
 
 ## Core Directives
 
-1. **Mandatory MCP Usage**: When `.genome/watcher.db` exists, you MUST use CodeGenome MCP access for all codebase, architecture, dependency, or symbol queries whenever it is available.
+1. **Mandatory MCP Usage**: When `.genome/codegenome.db` exists, you MUST use CodeGenome MCP access for all codebase, architecture, dependency, or symbol queries whenever it is available.
 2. **Access Order**: First use native CodeGenome MCP tools exposed in your context. If those tools are missing, you MAY try a local MCP HTTP endpoint such as `http://127.0.0.1:7331/mcp` when the user has started it or configured it. Treat this as MCP transport access, not as an arbitrary application HTTP API.
 3. **Prefer Graph over Grep**: Use graph-backed MCP tools instead of raw file searching (`grep`) or reading entire files blindly. The graph provides semantic understanding.
 4. **Fallback Gracefully**: If native MCP tools are missing and HTTP MCP access is unavailable, incompatible, or returns empty data, tell the user exactly what failed and what to configure. Then, if needed, read `.genome/graph.json` or `.genome/exports/*.md` before resorting to standard text searches.

diff --git a/.gitignore b/.gitignore
@@ -12,9 +12,9 @@ dist/
 build/
 *.spec
 
-# Watcher runtime artifacts
+# CodeGenome runtime artifacts
 .genome/
-watcher.db
+codegenome.db
 
 # OS / IDE
 .DS_Store

diff --git a/.vscode/cline_mcp_settings.json b/.vscode/cline_mcp_settings.json
@@ -0,0 +1,10 @@
+{
+  "mcpServers": {
+    "codegenome": {
+      "command": "codegenome",
+      "args": [
+        "mcp-start"
+      ]
+    }
+  }
+}
diff --git a/.vscode/mcp.json b/.vscode/mcp.json
@@ -0,0 +1,10 @@
+{
+  "mcpServers": {
+    "codegenome": {
+      "command": "codegenome",
+      "args": [
+        "mcp-start"
+      ]
+    }
+  }
+}
diff --git a/.windsurfrules b/.windsurfrules
@@ -4,7 +4,7 @@ You are operating within a repository analyzed by CodeGenome, an architectural k
 
 ## Core Directives
 
-1. **Mandatory MCP Usage**: When `.genome/watcher.db` exists, you MUST use CodeGenome MCP access for all codebase, architecture, dependency, or symbol queries whenever it is available.
+1. **Mandatory MCP Usage**: When `.genome/codegenome.db` exists, you MUST use CodeGenome MCP access for all codebase, architecture, dependency, or symbol queries whenever it is available.
 2. **Access Order**: First use native CodeGenome MCP tools exposed in your context. If those tools are missing, you MAY try a local MCP HTTP endpoint such as `http://127.0.0.1:7331/mcp` when the user has started it or configured it. Treat this as MCP transport access, not as an arbitrary application HTTP API.
 3. **Prefer Graph over Grep**: Use graph-backed MCP tools instead of raw file searching (`grep`) or reading entire files blindly. The graph provides semantic understanding.
 4. **Fallback Gracefully**: If native MCP tools are missing and HTTP MCP access is unavailable, incompatible, or returns empty data, tell the user exactly what failed and what to configure. Then, if needed, read `.genome/graph.json` or `.genome/exports/*.md` before resorting to standard text searches.

diff --git a/AGENTS.md b/AGENTS.md
@@ -4,7 +4,7 @@ You are operating within a repository analyzed by CodeGenome, an architectural k
 
 ## Core Directives
 
-1. **Mandatory MCP Usage**: When `.genome/watcher.db` exists, you MUST use CodeGenome MCP access for all codebase, architecture, dependency, or symbol queries whenever it is available.
+1. **Mandatory MCP Usage**: When `.genome/codegenome.db` exists, you MUST use CodeGenome MCP access for all codebase, architecture, dependency, or symbol queries whenever it is available.
 2. **Access Order**: First use native CodeGenome MCP tools exposed in your context. If those tools are missing, you MAY try a local MCP HTTP endpoint such as `http://127.0.0.1:7331/mcp` when the user has started it or configured it. Treat this as MCP transport access, not as an arbitrary application HTTP API.
 3. **Prefer Graph over Grep**: Use graph-backed MCP tools instead of raw file searching (`grep`) or reading entire files blindly. The graph provides semantic understanding.
 4. **Fallback Gracefully**: If native MCP tools are missing and HTTP MCP access is unavailable, incompatible, or returns empty data, tell the user exactly what failed and what to configure. Then, if needed, read `.genome/graph.json` or `.genome/exports/*.md` before resorting to standard text searches.

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -165,7 +165,7 @@ Graph artifacts are written under `.genome/` in the analyzed workspace. See [doc
 
 ### Optional: standalone binary
 
-To build a PyInstaller binary (named `watcher` in `dist/`):
+To build a PyInstaller binary (named `codegenome` in `dist/`):
 
 ```bash
 python build_cli.py
@@ -235,7 +235,7 @@ For MCP or client integration problems, also note which client (Cursor, Claude D
 
 ## Documentation
 
-When updating user-facing docs, use **`codegenome`** as the primary CLI name. Document legacy flag-based usage as `python -m codegenome --…`. The on-disk database file remains `.genome/watcher.db`.
+When updating user-facing docs, use **`codegenome`** as the primary CLI name. Document legacy flag-based usage as `python -m codegenome --…`. The on-disk database file remains `.genome/codegenome.db`.
 
 | Document | Purpose |
 |----------|---------|

diff --git a/CURSOR_MCP_SETUP.md b/CURSOR_MCP_SETUP.md
@@ -0,0 +1,33 @@
+# CodeGenome Cursor MCP Setup
+
+This project uses **CodeGenome** to provide an architectural knowledge graph that helps Cursor understand the codebase deeply.
+
+## Prerequisites
+
+1. Ensure `codegenome` is installed in your environment:
+   ```bash
+   pip install codegenome
+   ```
+2. You must generate the initial knowledge graph so that the `codegenome.db` exists. Run:
+   ```bash
+   codegenome analyze
+   ```
+   *Note: This repository is already configured to ignore `.genome/codegenome.db` in `.gitignore`.*
+
+## Cursor MCP Integration
+
+Cursor automatically reads the `.cursor/mcp.json` file in this repository. The configuration points to the `codegenome mcp-start` command. 
+
+Once Cursor connects to the MCP server, it will generate the necessary tool configurations under `.cursor/mcps/` automatically at runtime.
+
+### Troubleshooting
+
+- **Server Not Starting?** If Cursor cannot find the `codegenome` command, you may need to update the `command` field in `.cursor/mcp.json` to point to the absolute path of your `codegenome` executable (e.g., inside your virtual environment, like `.venv/bin/codegenome` or `.venv/Scripts/codegenome.exe`), or run Cursor from an activated terminal.
+- **Tools Missing?** Ensure that `.genome/codegenome.db` has been created by running `codegenome analyze`.
+
+## Continuous Updates
+
+To keep the CodeGenome knowledge graph updated automatically as you edit files, run the live codegenome in the background:
+```bash
+codegenome evolve --live
+```
diff --git a/README.md b/README.md
@@ -92,7 +92,7 @@ codegenome evolve --live --lan .
 ## 🛠️ Troubleshooting
 
 ### 1. "No graph found" or Missing Database
-**Symptom:** When attempting to run the MCP server (`codegenome mcp-start`) or export the graph (`codegenome export`), you receive an error that no graph was found or `.genome/watcher.db` does not exist.
+**Symptom:** When attempting to run the MCP server (`codegenome mcp-start`) or export the graph (`codegenome export`), you receive an error that no graph was found or `.genome/codegenome.db` does not exist.
 **Solution:** Codegenome needs to build its initial knowledge graph database before it can be served or exported. Always run `codegenome analyze .` in your workspace first to generate the graph.
 
 ### 2. "unrecognized arguments" CLI Error

diff --git a/build_cli.py b/build_cli.py
@@ -1,5 +1,5 @@
 #!/usr/bin/env python3
-"""Build a standalone watcher CLI binary with PyInstaller."""
+"""Build a standalone codegenome CLI binary with PyInstaller."""
 
 from __future__ import annotations
 
@@ -16,7 +16,7 @@
 BUILD = ROOT / "build"
 SPEC = ROOT / "codegenome.spec"
 
-BINARY_NAME = "watcher"
+BINARY_NAME = "codegenome"
 
 HIDDEN_IMPORTS = [
     "codegenome",
@@ -187,7 +187,7 @@ def build(*, clean: bool = True) -> Path:
 
 
 def parse_args(argv: list[str] | None = None) -> argparse.Namespace:
-    parser = argparse.ArgumentParser(description="Build watcher standalone binary")
+    parser = argparse.ArgumentParser(description="Build codegenome standalone binary")
     parser.add_argument(
         "--no-clean",
         action="store_true",

diff --git a/docs/cli-reference.md b/docs/cli-reference.md
@@ -13,7 +13,7 @@ Both operate on a **workspace** (project root). By default that is the current d
 
 | Path | Purpose |
 |------|---------|
-| `.genome/watcher.db` | Timeline snapshots (SQLite) |
+| `.genome/codegenome.db` | Timeline snapshots (SQLite) |
 | `.genome/graph.json` | Latest graph |
 | `.genome/exports/` | HTML, Markdown, GraphML, etc. |
 | `.genome/scan_cache.db` | Incremental scan cache |
@@ -240,7 +240,7 @@ Terminal 2:
 
 ```bash
 python -m codegenome.installer \
-  --db-path "$(pwd)/.genome/watcher.db" \
+  --db-path "$(pwd)/.genome/codegenome.db" \
   --client cursor \
   --transport http
 codegenome rules --client cursor .

diff --git a/docs/installation.md b/docs/installation.md
@@ -67,7 +67,7 @@ Codegenome writes artifacts under `<workspace>/.genome/`:
 | Path | Purpose |
 |------|---------|
 | `.genome/graph.json` | Latest graph |
-| `.genome/watcher.db` | Timeline snapshots (SQLite) |
+| `.genome/codegenome.db` | Timeline snapshots (SQLite) |
 | `.genome/exports/` | HTML, Markdown, GraphML, etc. |
 | `.genome/scan_cache.db` | Incremental scan cache |
 
@@ -93,7 +93,7 @@ python -m codegenome --workspace . --build --mcp --watch
 
 ```bash
 python -m codegenome.installer \
-  --db-path "$(pwd)/.genome/watcher.db" \
+  --db-path "$(pwd)/.genome/codegenome.db" \
   --client cursor \
   --transport http \
   --host 127.0.0.1 \
@@ -119,15 +119,15 @@ Or run the standalone server module:
 
 ```bash
 python -m codegenome.mcp_server \
-  --db-path ./.genome/watcher.db \
+  --db-path ./.genome/codegenome.db \
   --transport stdio
 ```
 
 See [MCP integration](mcp-integration.md) for environment variables, supported clients, and agent rules.
 
 ## Optional: standalone binary
 
-To build a PyInstaller binary named `watcher` in `dist/` (requires the `dev` extra):
+To build a PyInstaller binary named `codegenome` in `dist/` (requires the `dev` extra):
 
 ```bash
 python build_cli.py

diff --git a/docs/mcp-integration.md b/docs/mcp-integration.md
@@ -18,7 +18,7 @@ python -m codegenome --workspace . --build --mcp --watch
 
 # Terminal 2: install client config
 python -m codegenome.installer \
-  --db-path "$(pwd)/.genome/watcher.db" \
+  --db-path "$(pwd)/.genome/codegenome.db" \
   --client cursor \
   --transport http \
   --host 127.0.0.1 \
@@ -43,7 +43,7 @@ Or configure clients to run the module directly:
 
 ```bash
 python -m codegenome.mcp_server \
-  --db-path ./.genome/watcher.db \
+  --db-path ./.genome/codegenome.db \
   --transport stdio
 ```
 
@@ -56,14 +56,14 @@ python -m codegenome.mcp_server --help
 
 # HTTP
 python -m codegenome.mcp_server \
-  --db-path ./.genome/watcher.db \
+  --db-path ./.genome/codegenome.db \
   --host 127.0.0.1 \
   --port 7331 \
   --transport http
 
 # Stdio
 python -m codegenome.mcp_server \
-  --db-path ./.genome/watcher.db \
+  --db-path ./.genome/codegenome.db \
   --transport stdio
 ```
 
@@ -75,7 +75,7 @@ python -m codegenome.installer --help
 
 | Flag | Description |
 |------|-------------|
-| `--db-path PATH` | Absolute path to `.genome/watcher.db` |
+| `--db-path PATH` | Absolute path to `.genome/codegenome.db` |
 | `--python PATH` | Python executable for stdio transport |
 | `--transport stdio\|http` | Config transport mode |
 | `--host HOST` | HTTP host in config |
@@ -101,12 +101,12 @@ Always use **absolute paths** for `--db-path`.
 
 | Variable | Default | Purpose |
 |----------|---------|---------|
-| `WATCHER_MCP_DB_PATH` | `test.db` | Database path |
-| `WATCHER_MCP_HOST` | `127.0.0.1` | HTTP bind host |
-| `WATCHER_MCP_PORT` | `7331` | HTTP bind port |
-| `WATCHER_MCP_TRANSPORT` | `http` | `http` or `stdio` |
-| `WATCHER_MCP_TIMEOUT` | `30` | Tool timeout (seconds) |
-| `WATCHER_MCP_LOG_LEVEL` | `INFO` | Log level |
+| `CODEGENOME_MCP_DB_PATH` | `test.db` | Database path |
+| `CODEGENOME_MCP_HOST` | `127.0.0.1` | HTTP bind host |
+| `CODEGENOME_MCP_PORT` | `7331` | HTTP bind port |
+| `CODEGENOME_MCP_TRANSPORT` | `http` | `http` or `stdio` |
+| `CODEGENOME_MCP_TIMEOUT` | `30` | Tool timeout (seconds) |
+| `CODEGENOME_MCP_LOG_LEVEL` | `INFO` | Log level |
 
 ## Health check
 
@@ -129,8 +129,8 @@ Manual Cursor rule install:
 
 ```bash
 mkdir -p .cursor/rules
-sed 's/{{MCP_PORT}}/7331/g' extensions/templates/watcher-knowledge-graph.mdc \
-  > .cursor/rules/watcher-knowledge-graph.mdc
+sed 's/{{MCP_PORT}}/7331/g' extensions/templates/codegenome-knowledge-graph.mdc \
+  > .cursor/rules/codegenome-knowledge-graph.mdc
 ```
 
 On Windows PowerShell, copy the template and replace `{{MCP_PORT}}` with `7331` manually or use your editor's find-and-replace.
@@ -157,7 +157,7 @@ codegenome analyze .
 |---------|----------|
 | Connection refused | Run HTTP MCP (`python -m codegenome --mcp --build --watch`) or `mcp_server`; ensure the graph was built |
 | Port 7331 in use | Stop the other instance or run `mcp_server --port 7332` and update client config |
-| Empty tool results | Run `codegenome analyze .` first; confirm `.genome/watcher.db` exists |
+| Empty tool results | Run `codegenome analyze .` first; confirm `.genome/codegenome.db` exists |
 | Client not using MCP | Restart the client after `installer`; verify the config file path |
 | Stdio vs HTTP mismatch | Match `--transport` in `installer` with how the server is started |
 

diff --git a/extensions/README.md b/extensions/README.md
@@ -6,7 +6,7 @@ This folder holds **editor and agent integration assets** that ship with the Cod
 
 | Path | Purpose |
 |------|---------|
-| `templates/watcher-knowledge-graph.mdc` | Cursor rule template — teaches agents to use Codegenome MCP tools |
+| `templates/codegenome-knowledge-graph.mdc` | Cursor rule template — teaches agents to use Codegenome MCP tools |
 | `templates/copilot-instructions.md` | GitHub Copilot instructions template |
 | `templates/claude-instructions.md` | Claude-oriented instructions template |
 
@@ -32,7 +32,7 @@ Write MCP server entries into AI client config files:
 
 ```bash
 python -m codegenome.installer \
-  --db-path /absolute/path/to/project/.genome/watcher.db \
+  --db-path /absolute/path/to/project/.genome/codegenome.db \
   --client cursor \
   --transport http \
   --host 127.0.0.1 \
@@ -47,8 +47,8 @@ See [MCP integration](../docs/mcp-integration.md) for transport modes, health ch
 
 ```bash
 mkdir -p .cursor/rules
-sed 's/{{MCP_PORT}}/7331/g' extensions/templates/watcher-knowledge-graph.mdc \
-  > .cursor/rules/watcher-knowledge-graph.mdc
+sed 's/{{MCP_PORT}}/7331/g' extensions/templates/codegenome-knowledge-graph.mdc \
+  > .cursor/rules/codegenome-knowledge-graph.mdc
 ```
 
 Restart Cursor after installing MCP config or rules.

diff --git a/extensions/templates/claude-instructions.md b/extensions/templates/claude-instructions.md
@@ -4,7 +4,7 @@ You are operating within a repository analyzed by CodeGenome, an architectural k
 
 ## Core Directives
 
-1. **Mandatory MCP Usage**: When `.genome/watcher.db` exists, you MUST use CodeGenome MCP access for all codebase, architecture, dependency, or symbol queries whenever it is available.
+1. **Mandatory MCP Usage**: When `.genome/codegenome.db` exists, you MUST use CodeGenome MCP access for all codebase, architecture, dependency, or symbol queries whenever it is available.
 2. **Access Order**: First use native CodeGenome MCP tools exposed in your context. If those tools are missing, you MAY try a local MCP HTTP endpoint such as `http://127.0.0.1:{{MCP_PORT}}/mcp` when the user has started it or configured it. Treat this as MCP transport access, not as an arbitrary application HTTP API.
 3. **Prefer Graph over Grep**: Use graph-backed MCP tools instead of raw file searching (`grep`) or reading entire files blindly. The graph provides semantic understanding.
 4. **Fallback Gracefully**: If native MCP tools are missing and HTTP MCP access is unavailable, incompatible, or returns empty data, tell the user exactly what failed and what to configure. Then, if needed, read `.genome/graph.json` or `.genome/exports/*.md` before resorting to standard text searches.

diff --git a/...ons/templates/watcher-knowledge-graph.mdc → .../templates/codegenome-knowledge-graph.mdc b/...ons/templates/watcher-knowledge-graph.mdc → .../templates/codegenome-knowledge-graph.mdc
@@ -9,7 +9,7 @@ You are operating within a repository analyzed by CodeGenome, an architectural k
 
 ## Core Directives
 
-1. **Mandatory MCP Usage**: When `.genome/watcher.db` exists, you MUST use CodeGenome MCP access for all codebase, architecture, dependency, or symbol queries whenever it is available.
+1. **Mandatory MCP Usage**: When `.genome/codegenome.db` exists, you MUST use CodeGenome MCP access for all codebase, architecture, dependency, or symbol queries whenever it is available.
 2. **Access Order**: First use native CodeGenome MCP tools exposed in your context. If those tools are missing, you MAY try a local MCP HTTP endpoint such as `http://127.0.0.1:{{MCP_PORT}}/mcp` when the user has started it or configured it. Treat this as MCP transport access, not as an arbitrary application HTTP API.
 3. **Prefer Graph over Grep**: Use graph-backed MCP tools instead of raw file searching (`grep`) or reading entire files blindly. The graph provides semantic understanding.
 4. **Fallback Gracefully**: If native MCP tools are missing and HTTP MCP access is unavailable, incompatible, or returns empty data, tell the user exactly what failed and what to configure. Then, if needed, read `.genome/graph.json` or `.genome/exports/*.md` before resorting to standard text searches.

diff --git a/extensions/templates/copilot-instructions.md b/extensions/templates/copilot-instructions.md
@@ -4,7 +4,7 @@ You are operating within a repository analyzed by CodeGenome, an architectural k
 
 ## Core Directives
 
-1. **Mandatory MCP Usage**: When `.genome/watcher.db` exists, you MUST use CodeGenome MCP access for all codebase, architecture, dependency, or symbol queries whenever it is available.
+1. **Mandatory MCP Usage**: When `.genome/codegenome.db` exists, you MUST use CodeGenome MCP access for all codebase, architecture, dependency, or symbol queries whenever it is available.
 2. **Access Order**: First use native CodeGenome MCP tools exposed in your context. If those tools are missing, you MAY try a local MCP HTTP endpoint such as `http://127.0.0.1:{{MCP_PORT}}/mcp` when the user has started it or configured it. Treat this as MCP transport access, not as an arbitrary application HTTP API.
 3. **Prefer Graph over Grep**: Use graph-backed MCP tools instead of raw file searching (`grep`) or reading entire files blindly. The graph provides semantic understanding.
 4. **Fallback Gracefully**: If native MCP tools are missing and HTTP MCP access is unavailable, incompatible, or returns empty data, tell the user exactly what failed and what to configure. Then, if needed, read `.genome/graph.json` or `.genome/exports/*.md` before resorting to standard text searches.