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Patch Summary for branch v.0.1.5---patch

Commits

  • 75e3a4e - Rebrand Watcher to CodeGenome and update configs (Md. Fatin Shadab Turja)
  • efa56ca - patch (Md. Fatin Shadab Turja)

Changed Files

 .cursor/mcp.json                                   | 10 +++++++
 ...ge-graph.mdc => codegenome-knowledge-graph.mdc} |  2 +-
 .github/copilot-instructions.md                    |  2 +-
 .gitignore                                         |  4 +--
 .vscode/cline_mcp_settings.json                    | 10 +++++++
 .vscode/mcp.json                                   | 10 +++++++
 .windsurfrules                                     |  2 +-
 AGENTS.md                                          |  2 +-
 CONTRIBUTING.md                                    |  4 +--
 CURSOR_MCP_SETUP.md                                | 33 ++++++++++++++++++++++
 README.md                                          |  2 +-
 build_cli.py                                       |  6 ++--
 docs/cli-reference.md                              |  4 +--
 docs/installation.md                               |  8 +++---
 docs/mcp-integration.md                            | 28 +++++++++---------
 extensions/README.md                               |  8 +++---
 extensions/templates/claude-instructions.md        |  2 +-
 ...ge-graph.mdc => codegenome-knowledge-graph.mdc} |  2 +-
 extensions/templates/copilot-instructions.md       |  2 +-
 pyproject.toml                                     | 10 +++----
 src/codegenome/__init__.py                         |  6 ++--
 src/codegenome/__main__.py                         | 18 ++++++------
 src/codegenome/ai_chat.py                          |  2 +-
 src/codegenome/assets/html/graph-viewer.js         |  4 +--
 src/codegenome/builder.py                          |  2 +-
 src/codegenome/cli.py                              | 22 +++++++--------
 src/codegenome/clusterer.py                        |  2 +-
 src/codegenome/{watcher.py => core.py}             | 30 ++++++++++----------
 src/codegenome/exporter.py                         | 10 +++----
 src/codegenome/graph_store.py                      |  4 +--
 src/codegenome/installer.py                        | 12 ++++----
 src/codegenome/intelligence.py                     |  4 +--
 src/codegenome/live_graph_monitor.py               |  8 +++---
 src/codegenome/mcp_server.py                       | 18 ++++++------
 src/codegenome/parser.py                           |  4 +--
 src/codegenome/rules.py                            |  4 +--
 src/codegenome/templates/graph.html.j2             |  2 +-
 src/codegenome/templates/rules/cursor-rules.mdc    |  2 +-
 .../templates/rules/markdown-instructions.md       |  2 +-
 src/codegenome/timeline.py                         |  2 +-
 test2.py                                           | 13 +++++++++
 tests/test_mcp_server.py                           |  2 +-
 42 files changed, 200 insertions(+), 124 deletions(-)

Diff

diff --git a/.cursor/mcp.json b/.cursor/mcp.json
new file mode 100644
index 0000000..82adbbd
--- /dev/null
+++ b/.cursor/mcp.json
@@ -0,0 +1,10 @@
+{
+  "mcpServers": {
+    "codegenome": {
+      "command": "codegenome",
+      "args": [
+        "mcp-start"
+      ]
+    }
+  }
+}
diff --git a/.cursor/rules/watcher-knowledge-graph.mdc b/.cursor/rules/codegenome-knowledge-graph.mdc
similarity index 92%
rename from .cursor/rules/watcher-knowledge-graph.mdc
rename to .cursor/rules/codegenome-knowledge-graph.mdc
index 42b7600..76b5bd3 100644
--- a/.cursor/rules/watcher-knowledge-graph.mdc
+++ b/.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
index b512202..5e4ae97 100644
--- 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
index f924f6f..6d1d34c 100644
--- 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
new file mode 100644
index 0000000..82adbbd
--- /dev/null
+++ 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
new file mode 100644
index 0000000..82adbbd
--- /dev/null
+++ b/.vscode/mcp.json
@@ -0,0 +1,10 @@
+{
+  "mcpServers": {
+    "codegenome": {
+      "command": "codegenome",
+      "args": [
+        "mcp-start"
+      ]
+    }
+  }
+}
diff --git a/.windsurfrules b/.windsurfrules
index b512202..5e4ae97 100644
--- 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
index b512202..5e4ae97 100644
--- 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
index 7a1a6eb..32ae667 100644
--- 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
new file mode 100644
index 0000000..19b0180
--- /dev/null
+++ 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
index e562be8..b53e59d 100644
--- 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
index dd99e63..9ac60b6 100644
--- 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 @@ DIST = ROOT / "dist"
 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
index 56a7c9f..7a31eab 100644
--- 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
index a697da8..adfe7f1 100644
--- 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 \
@@ -119,7 +119,7 @@ Or run the standalone server module:
 
 ```bash
 python -m codegenome.mcp_server \
-  --db-path ./.genome/watcher.db \
+  --db-path ./.genome/codegenome.db \
   --transport stdio

@@ -127,7 +127,7 @@ See MCP integration for environment variables, supported c

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):

python build_cli.py
diff --git a/docs/mcp-integration.md b/docs/mcp-integration.md
index ed75076..d04a02f 100644
--- 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 index 073a1a2..19bcd58 100644 --- 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
+ templates/codegenome-knowledge-graph.mdc
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:

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 index 3666328..a959330 100644 --- 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/extensions/templates/watcher-knowledge-graph.mdc b/extensions/templates/codegenome-knowledge-graph.mdc similarity index 92% rename from extensions/templates/watcher-knowledge-graph.mdc rename to extensions/templates/codegenome-knowledge-graph.mdc index 6796262..dab6019 100644 --- a/extensions/templates/watcher-knowledge-graph.mdc +++ b/extensions/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 index 3666328..a959330 100644 --- 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. diff --git a/pyproject.toml b/pyproject.toml index dc9c188..76fd884 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -9,7 +9,7 @@ description = "Open-source CLI for building and querying local codebase knowledg readme = "README.md" license = "MIT" requires-python = ">=3.11" -authors = [{ name = "Watcher Contributors" }] +authors = [{ name = "CodeGenome Contributors" }] keywords = ["code-analysis", "knowledge-graph", "mcp", "cli", "tree-sitter"] classifiers = [ "Development Status :: 3 - Alpha", @@ -52,10 +52,10 @@ dependencies = [ dev = ["pytest", "pytest-cov", "ruff", "pyinstaller>=6.0,<7"]

[project.urls] -Homepage = "https://github.com/watcher-dev/codegenome" -Documentation = "https://github.com/watcher-dev/codegenome#readme" -Repository = "https://github.com/watcher-dev/codegenome" -Issues = "https://github.com/watcher-dev/codegenome/issues" +Homepage = "https://github.com/codegenome-dev/codegenome" +Documentation = "https://github.com/codegenome-dev/codegenome#readme" +Repository = "https://github.com/codegenome-dev/codegenome" +Issues = "https://github.com/codegenome-dev/codegenome/issues"

[project.scripts] codegenome = "codegenome.cli:cli" diff --git a/src/codegenome/init.py b/src/codegenome/init.py index 391fc78..5609da8 100644 --- a/src/codegenome/init.py +++ b/src/codegenome/init.py @@ -12,7 +12,7 @@ from .parser import ParseResult, SourceParser from .scanner import ScanResult, WorkspaceScanner from .timeline import GraphDelta, GraphTimeline, SnapshotInfo from .version import version -from .watcher import BuildResult, WatcherConfig, WatcherEngine +from .core import BuildResult, CodeGenomeConfig, CodeGenomeEngine

all = [ "version", @@ -31,7 +31,7 @@ all = [ "SnapshotInfo", "SourceParser", "SUPPORTED_FORMATS",

  • "WatcherConfig",
  • "WatcherEngine",
  • "CodeGenomeConfig",
  • "CodeGenomeEngine", "WorkspaceScanner", ] diff --git a/src/codegenome/main.py b/src/codegenome/main.py index 5f6606e..6542aaa 100644 --- a/src/codegenome/main.py +++ b/src/codegenome/main.py @@ -1,4 +1,4 @@ -"""CLI entry point for Watcher.""" +"""CLI entry point for CodeGenome."""

from future import annotations

@@ -9,13 +9,13 @@ import sys from pathlib import Path

from codegenome.exporter import SUPPORTED_FORMATS -from codegenome.watcher import WatcherConfig, WatcherEngine +from codegenome.core import CodeGenomeConfig, CodeGenomeEngine

LOG = logging.getLogger("codegenome")

def parse_args(argv: list[str] | None = None) -> argparse.Namespace:

  • """Parse command line arguments for the Watcher CLI.

  • """Parse command line arguments for the CodeGenome CLI.

    Args: argv (list[str] | None, optional): List of command line arguments. Defaults to None, @@ -24,7 +24,7 @@ def parse_args(argv: list[str] | None = None) -> argparse.Namespace: Returns: argparse.Namespace: The parsed command line arguments. """

  • parser = argparse.ArgumentParser(description="Watcher CLI — local codebase knowledge graph")
  • parser = argparse.ArgumentParser(description="CodeGenome CLI — local codebase knowledge graph") parser.add_argument( "--workspace", default=".", @@ -78,7 +78,7 @@ def parse_args(argv: list[str] | None = None) -> argparse.Namespace: parser.add_argument( "--db-path", default=None,
  •    help="Timeline SQLite database path (default: .genome/watcher.db)",

  •    help="Timeline SQLite database path (default: .genome/codegenome.db)",

    ) parser.add_argument( "--mcp", @@ -149,7 +149,7 @@ def run_timeline_query(args: argparse.Namespace) -> int: from codegenome.graph_store import GraphStore, GraphStoreError

    workspace = Path(args.workspace).resolve()

  • db_path = Path(args.db_path).resolve() if args.db_path else workspace / ".genome" / "watcher.db"

  • db_path = Path(args.db_path).resolve() if args.db_path else workspace / ".genome" / "codegenome.db"

    store = GraphStore(db_path) try: @@ -186,7 +186,7 @@ def run_timeline_query(args: argparse.Namespace) -> int:

def main(argv: list[str] | None = None) -> int:

  • """Main entry point for the codegenome Watcher CLI.

  • """Main entry point for the codegenome CodeGenome CLI.

    Args: argv (list[str] | None, optional): List of command line arguments. Defaults to None. @@ -232,7 +232,7 @@ def main(argv: list[str] | None = None) -> int: print("Nothing to do. Pass --build, --watch, and/or --live-graph.", file=sys.stderr) return 1

  • config = WatcherConfig(
  • config = CodeGenomeConfig( workspace=workspace, db_path=Path(args.db_path).resolve() if args.db_path else None, export_formats=tuple(fmt.lower() for fmt in args.export), @@ -241,7 +241,7 @@ def main(argv: list[str] | None = None) -> int: live_graph=args.live_graph, live_graph_poll_seconds=max(1.0, float(args.live_graph_interval)), )
  • engine = WatcherEngine(config)

  • engine = CodeGenomeEngine(config)

    try: if args.build or args.watch or args.live_graph: diff --git a/src/codegenome/ai_chat.py b/src/codegenome/ai_chat.py index e6752ca..eccb141 100644 --- a/src/codegenome/ai_chat.py +++ b/src/codegenome/ai_chat.py @@ -102,7 +102,7 @@ CONTEXT_PROFILES = { } DEFAULT_HTTP_HEADERS = { "Accept": "application/json",

diff --git a/src/codegenome/assets/html/graph-viewer.js b/src/codegenome/assets/html/graph-viewer.js index c179b6d..db8eaf0 100644 --- a/src/codegenome/assets/html/graph-viewer.js +++ b/src/codegenome/assets/html/graph-viewer.js @@ -152,7 +152,7 @@

 if (window.location.protocol === 'file:') {
   setLivePending(false);

  •  showToast('Open via Watcher extension for live updates.');

  •  showToast('Open via CodeGenome extension for live updates.');
 return;
    }

@@ -183,7 +183,7 @@ }

function readEmbeddedGraph() {

  • const element = document.getElementById('watcher-graph-data');
  • const element = document.getElementById('codegenome-graph-data'); if (!element || !element.textContent) { return null; } diff --git a/src/codegenome/builder.py b/src/codegenome/builder.py index e8ac0cf..d49dfdc 100644 --- a/src/codegenome/builder.py +++ b/src/codegenome/builder.py @@ -1,4 +1,4 @@ -"""NetworkX graph builder for Watcher scan and parse results.""" +"""NetworkX graph builder for CodeGenome scan and parse results."""

from future import annotations

diff --git a/src/codegenome/cli.py b/src/codegenome/cli.py index 1b80560..e568248 100644 --- a/src/codegenome/cli.py +++ b/src/codegenome/cli.py @@ -4,7 +4,7 @@ import sys from pathlib import Path import click

-from codegenome.watcher import WatcherEngine, WatcherConfig +from codegenome.core import CodeGenomeEngine, CodeGenomeConfig

@click.group() def cli(): @@ -21,8 +21,8 @@ def analyze(path: str): """ click.echo(f"Analyzing workspace at {path}...") workspace = Path(path).resolve()

  • config = WatcherConfig(workspace=workspace, export_formats=("json",))
  • engine = WatcherEngine(config)

  • config = CodeGenomeConfig(workspace=workspace, export_formats=("json",))

  • engine = CodeGenomeEngine(config)

    def on_progress(message: str) -> None: click.echo(message) @@ -59,12 +59,12 @@ def export(export_format: str, path: str): path (str): The workspace directory path to export from. """ workspace = Path(path).resolve()

  • config = WatcherConfig(workspace=workspace)
  • engine = WatcherEngine(config)

  • config = CodeGenomeConfig(workspace=workspace)

  • engine = CodeGenomeEngine(config)

    try: # Check if the graph exists. If not loaded, it means it hasn't been analyzed.

  •    # engine._load_existing_graph() is called in WatcherEngine.__init__.

  •    # engine._load_existing_graph() is called in CodeGenomeEngine.__init__.
   # Alternatively, we can check if the graph has nodes.
   if engine.builder.graph.number_of_nodes() == 0:
       click.echo("Error: No graph found. Please run 'codegenome analyze' first before exporting.", err=True)

@@ -119,8 +119,8 @@ def mcp_start(path: str, transport: str, port: int, lan: bool): lan (bool): Whether to expose HTTP transport on the local network. """ workspace = Path(path).resolve()

  • config = WatcherConfig(workspace=workspace)
  • engine = WatcherEngine(config)
  • config = CodeGenomeConfig(workspace=workspace)
  • engine = CodeGenomeEngine(config) db_path = engine.db_path engine.close() # Close the engine since the MCP server process will open its own connection

@@ -159,11 +159,11 @@ def evolve(path: str, live: bool, lan: bool): from socketserver import ThreadingTCPServer from watchdog.observers import Observer from codegenome.ai_chat import AIChatError, chat_completion, load_models, settings_payload

  • from codegenome.watcher import WatcherConfig, WatcherEngine, SurgicalUpdateHandler

  • from codegenome.core import CodeGenomeConfig, CodeGenomeEngine, SurgicalUpdateHandler

    workspace = Path(path).resolve()

  • config = WatcherConfig(workspace=workspace, export_formats=("json", "html"))
  • engine = WatcherEngine(config)

  • config = CodeGenomeConfig(workspace=workspace, export_formats=("json", "html"))

  • engine = CodeGenomeEngine(config)

    click.echo(f"Running initial build for {workspace}...") engine.build(full=False) diff --git a/src/codegenome/clusterer.py b/src/codegenome/clusterer.py index 323147c..ae0b8c7 100644 --- a/src/codegenome/clusterer.py +++ b/src/codegenome/clusterer.py @@ -1,4 +1,4 @@ -"""Leiden community detection and bridge-node analysis for Watcher graphs.""" +"""Leiden community detection and bridge-node analysis for CodeGenome graphs."""

from future import annotations

diff --git a/src/codegenome/watcher.py b/src/codegenome/core.py similarity index 95% rename from src/codegenome/watcher.py rename to src/codegenome/core.py index 07d0c3e..fc0e406 100644 --- a/src/codegenome/watcher.py +++ b/src/codegenome/core.py @@ -1,4 +1,4 @@ -"""WatcherEngine orchestration for builds, watching, MCP, and exports.""" +"""CodeGenomeEngine orchestration for builds, watching, MCP, and exports."""

from future import annotations

@@ -35,8 +35,8 @@ PARSE_PROGRESS_INTERVAL = 50

@dataclass -class WatcherConfig:

  • """Configuration for WatcherEngine.""" +class CodeGenomeConfig:

  • """Configuration for CodeGenomeEngine."""

    workspace: Path db_path: Path | None = None @@ -53,7 +53,7 @@ class WatcherConfig:

@dataclass class BuildResult:

  • """Container for the output of a WatcherEngine build or update."""

  • """Container for the output of a CodeGenomeEngine build or update."""

    graph: nx.DiGraph report: IntelligenceReport @@ -64,11 +64,11 @@ class BuildResult: class _RebuildHandler(FileSystemEventHandler): """File system event handler to trigger incremental rebuilds with debouncing."""

  • def init(self, engine: WatcherEngine, debounce_seconds: float) -> None:

  • def init(self, engine: CodeGenomeEngine, debounce_seconds: float) -> None: """Initialize the _RebuildHandler.

    Args:

  •        engine (WatcherEngine): The engine to invoke rebuilds on.

  •        engine (CodeGenomeEngine): The engine to invoke rebuilds on.
       debounce_seconds (float): Delay in seconds before triggering a rebuild.
   """
   self._engine = engine

@@ -108,17 +108,17 @@ class _RebuildHandler(FileSystemEventHandler): ) try: self._engine.rebuild_incremental()

  •    except Exception:  # noqa: BLE001 - keep watcher alive

  •    except Exception:  # noqa: BLE001 - keep codegenome alive
       LOG.exception("Incremental rebuild failed")

class SurgicalUpdateHandler(FileSystemEventHandler): """Surgically update the graph on individual file changes."""

  • def init(self, engine: WatcherEngine, live_server=None) -> None:

  • def init(self, engine: CodeGenomeEngine, live_server=None) -> None: """Initialize the SurgicalUpdateHandler.

    Args:

  •        engine (WatcherEngine): The engine performing graph updates.

  •        engine (CodeGenomeEngine): The engine performing graph updates.
       live_server (LiveGraphServer | None, optional): Server for real-time broadcasts. Defaults to None.
   """
   self._engine = engine

@@ -168,19 +168,19 @@ class SurgicalUpdateHandler(FileSystemEventHandler): LOG.exception(f"Surgical update failed for {event.src_path}")

-class WatcherEngine: +class CodeGenomeEngine: """Coordinate scanning, graph building, exports, watching, and MCP startup."""

  • def init(self, config: WatcherConfig) -> None:
  •    """Initialize the WatcherEngine.
  • def init(self, config: CodeGenomeConfig) -> None:
  •    """Initialize the CodeGenomeEngine.

   Args:

  •        config (WatcherConfig): The configuration defining paths and options.

  •        config (CodeGenomeConfig): The configuration defining paths and options.
   """
   self.config = config
   self.workspace = config.workspace.resolve()
   self.genome_dir = self.workspace / ".genome"

  •    self.db_path = (config.db_path or self.genome_dir / "watcher.db").resolve()

  •    self.db_path = (config.db_path or self.genome_dir / "codegenome.db").resolve()
   self.export_dir = (config.export_dir or self.genome_dir / "exports").resolve()
   self.graph_json_path = (
       config.graph_json_path or self.genome_dir / "graph.json"

@@ -479,7 +479,7 @@ class WatcherEngine: sys.stderr.write(line) sys.stderr.flush()

  •    thread = threading.Thread(target=forward, name="watcher-mcp-stderr", daemon=True)

  •    thread = threading.Thread(target=forward, name="codegenome-mcp-stderr", daemon=True)
   thread.start()

    def stop_mcp(self) -> None: diff --git a/src/codegenome/exporter.py b/src/codegenome/exporter.py index a7320b2..e2d1591 100644 --- a/src/codegenome/exporter.py +++ b/src/codegenome/exporter.py @@ -1,4 +1,4 @@ -"""Export Watcher graphs to JSON, HTML, GraphML, Cypher, Markdown, and Obsidian.""" +"""Export CodeGenome graphs to JSON, HTML, GraphML, Cypher, Markdown, and Obsidian."""

from future import annotations

@@ -65,7 +65,7 @@ class GraphStatistics:

@dataclass class GraphExporter:

  • """Serialize Watcher graphs and intelligence into multiple formats.

  • """Serialize CodeGenome graphs and intelligence into multiple formats.

    Attributes: graph (Graph): The graph instance to be exported. @@ -212,7 +212,7 @@ class GraphExporter: Path: The path to the successfully created Cypher file. """ lines = [

  •        "// Watcher graph export for Neo4j",

  •        "// CodeGenome graph export for Neo4j",
       f"// workspace: {self.workspace_name}",
       "",
   ]

@@ -294,7 +294,7 @@ class GraphExporter: )

     index_lines = [

  •        "# Watcher Graph Vault",

  •        "# CodeGenome Graph Vault",
       "",
       f"Workspace: `{self.workspace_name}`",
       "",

@@ -313,7 +313,7 @@ class GraphExporter: f"- Circular dependency groups: {len(self.report.circular_dependencies)}", ] )

  •    vault_root.joinpath("Watcher Index.md").write_text(

  •    vault_root.joinpath("CodeGenome Index.md").write_text(
       "\n".join(index_lines) + "\n",
       encoding="utf-8",
   )

diff --git a/src/codegenome/graph_store.py b/src/codegenome/graph_store.py index cfbd9a5..25b0592 100644 --- a/src/codegenome/graph_store.py +++ b/src/codegenome/graph_store.py @@ -1,4 +1,4 @@ -"""Graph query layer for the Watcher MCP server.""" +"""Graph query layer for the CodeGenome MCP server."""

from future import annotations

@@ -37,7 +37,7 @@ class GraphSummary:

class GraphStore:

  • """Load and query a Watcher timeline database.

  • """Load and query a CodeGenome timeline database.

    Provides a high-level API to interact with versioned graph snapshots, perform queries, and extract code intelligence metrics. diff --git a/src/codegenome/installer.py b/src/codegenome/installer.py index 57466d5..b60f4aa 100644 --- a/src/codegenome/installer.py +++ b/src/codegenome/installer.py @@ -1,4 +1,4 @@ -"""Install Watcher MCP server configs for common AI coding clients.""" +"""Install CodeGenome MCP server configs for common AI coding clients."""

from future import annotations

@@ -257,10 +257,10 @@ def parse_args(argv: list[str] | None = None) -> argparse.Namespace: Returns: argparse.Namespace: The parsed command-line arguments. """

  • parser = argparse.ArgumentParser(description="Install Watcher MCP configs for AI clients")
  • parser = argparse.ArgumentParser(description="Install CodeGenome MCP configs for AI clients") parser.add_argument( "--db-path",
  •    default=os.getenv("WATCHER_MCP_DB_PATH", "test.db"),

  •    default=os.getenv("CODEGENOME_MCP_DB_PATH", "test.db"),
   help="Timeline database path passed to the MCP server",
    ) parser.add_argument( @@ -271,18 +271,18 @@ def parse_args(argv: list[str] | None = None) -> argparse.Namespace: parser.add_argument( "--transport", choices=("stdio", "http"),
  •    default=os.getenv("WATCHER_MCP_TRANSPORT", "stdio"),

  •    default=os.getenv("CODEGENOME_MCP_TRANSPORT", "stdio"),
   help="Transport mode written into client configs",
    ) parser.add_argument( "--host",
  •    default=os.getenv("WATCHER_MCP_HOST", "127.0.0.1"),

  •    default=os.getenv("CODEGENOME_MCP_HOST", "127.0.0.1"),
   help="Host used for HTTP transport configs",
    ) parser.add_argument( "--port", type=int,
  •    default=int(os.getenv("WATCHER_MCP_PORT", "7331")),

  •    default=int(os.getenv("CODEGENOME_MCP_PORT", "7331")),
   help="Port used for HTTP transport configs",
    ) parser.add_argument( diff --git a/src/codegenome/intelligence.py b/src/codegenome/intelligence.py index 583f45a..f4260bf 100644 --- a/src/codegenome/intelligence.py +++ b/src/codegenome/intelligence.py @@ -1,4 +1,4 @@ -"""Architectural intelligence analysis over Watcher dependency graphs. +"""Architectural intelligence analysis over CodeGenome dependency graphs.

This module provides tools for analyzing a dependency graph and deriving actionable architectural signals such as dead code detection, circular @@ -40,7 +40,7 @@ class IntelligenceReport:

class GraphIntelligence:

  • """Derive actionable architectural signals from a Watcher graph.

  • """Derive actionable architectural signals from a CodeGenome graph.

    This class provides various methods to analyze the codebase graph and detect issues like dead code, god nodes, and circular dependencies. diff --git a/src/codegenome/live_graph_monitor.py b/src/codegenome/live_graph_monitor.py index 3dbc851..0e24d4f 100644 --- a/src/codegenome/live_graph_monitor.py +++ b/src/codegenome/live_graph_monitor.py @@ -14,7 +14,7 @@ from codegenome.workspace_metrics import ( )

if TYPE_CHECKING:

  • from codegenome.watcher import WatcherEngine
  • from codegenome.core import CodeGenomeEngine

LOG = logging.getLogger(name)

@@ -24,13 +24,13 @@ class LiveGraphMonitor:

 def __init__(
     self,

  •    engine: WatcherEngine,

  •    engine: CodeGenomeEngine,
   poll_interval_seconds: float,

    ) -> None: """Initialize the LiveGraphMonitor.

       Args:

  •        engine (WatcherEngine): The engine used for checking and rebuilding the graph.

  •        engine (CodeGenomeEngine): The engine used for checking and rebuilding the graph.
       poll_interval_seconds (float): Interval in seconds between polls.
   """
   self._engine = engine

@@ -52,7 +52,7 @@ class LiveGraphMonitor: ) self._thread = threading.Thread( target=self._poll_loop,

  •        name="watcher-live-graph",

  •        name="codegenome-live-graph",
       daemon=True,
   )
   self._thread.start()

diff --git a/src/codegenome/mcp_server.py b/src/codegenome/mcp_server.py index 5d2dd25..4a96a57 100644 --- a/src/codegenome/mcp_server.py +++ b/src/codegenome/mcp_server.py @@ -1,4 +1,4 @@ -"""FastMCP server exposing Watcher graph tools over localhost HTTP or stdio.""" +"""FastMCP server exposing CodeGenome graph tools over localhost HTTP or stdio."""

from future import annotations

@@ -31,12 +31,12 @@ DEFAULT_PORT = 7331 DEFAULT_TIMEOUT_SECONDS = 30.0 DEFAULT_TRANSPORT: Literal["http", "stdio"] = "http"

-ENV_HOST = "WATCHER_MCP_HOST" -ENV_PORT = "WATCHER_MCP_PORT" -ENV_DB_PATH = "WATCHER_MCP_DB_PATH" -ENV_TIMEOUT = "WATCHER_MCP_TIMEOUT" -ENV_LOG_LEVEL = "WATCHER_MCP_LOG_LEVEL" -ENV_TRANSPORT = "WATCHER_MCP_TRANSPORT" +ENV_HOST = "CODEGENOME_MCP_HOST" +ENV_PORT = "CODEGENOME_MCP_PORT" +ENV_DB_PATH = "CODEGENOME_MCP_DB_PATH" +ENV_TIMEOUT = "CODEGENOME_MCP_TIMEOUT" +ENV_LOG_LEVEL = "CODEGENOME_MCP_LOG_LEVEL" +ENV_TRANSPORT = "CODEGENOME_MCP_TRANSPORT"

F = TypeVar("F", bound=Callable[..., Any])

@@ -204,7 +204,7 @@ class GraphService: self.config = config self._lock = threading.RLock() self._store = GraphStore(config.db_path)

  •    self._executor = ThreadPoolExecutor(max_workers=4, thread_name_prefix="watcher-mcp")

  •    self._executor = ThreadPoolExecutor(max_workers=4, thread_name_prefix="codegenome-mcp")

    @property def store(self) -> GraphStore: @@ -470,7 +470,7 @@ def create_server( summary = service.run(service.store.summary) payload = { "status": "ok",

  •        "service": "watcher-mcp",

  •        "service": "codegenome-mcp",
       "version": __version__,
       "db_path": str(service.config.db_path),
       "snapshot_id": summary.snapshot_id,

diff --git a/src/codegenome/parser.py b/src/codegenome/parser.py index 3ce5646..5053aca 100644 --- a/src/codegenome/parser.py +++ b/src/codegenome/parser.py @@ -243,10 +243,10 @@ class SourceParser: self._parsers: dict[str, Parser] = {} for key, language in self._languages.items(): try:

  •            parser = Parser(language)

  •        except TypeError:
           parser = Parser()
           parser.set_language(language)

  •        except AttributeError:

  •            parser = Parser(language)
       self._parsers[key] = parser

    def detect_language(self, path: Path | str) -> str | None: diff --git a/src/codegenome/rules.py b/src/codegenome/rules.py index 903b4be..f71c852 100644 --- a/src/codegenome/rules.py +++ b/src/codegenome/rules.py @@ -1,4 +1,4 @@ -"""Generate Watcher AI agent rules and instructions.""" +"""Generate CodeGenome AI agent rules and instructions."""

from future import annotations

@@ -42,7 +42,7 @@ def rule_targets(workspace: Path | None = None) -> list[RuleTarget]: RuleTarget( key="cursor", label="Cursor",

  •        output_path=workspace / ".cursor" / "rules" / "watcher-knowledge-graph.mdc",

  •        output_path=workspace / ".cursor" / "rules" / "codegenome-knowledge-graph.mdc",
       template_name="cursor-rules.mdc",
   ),
   RuleTarget(

diff --git a/src/codegenome/templates/graph.html.j2 b/src/codegenome/templates/graph.html.j2 index 1624aa1..6dd7c93 100644 --- a/src/codegenome/templates/graph.html.j2 +++ b/src/codegenome/templates/graph.html.j2 @@ -1029,7 +1029,7 @@ 

 <script type="text/javascript">

  •    // Parse raw payload exported directly from SQLite and Watcher engine

  •    // Parse raw payload exported directly from SQLite and CodeGenome engine
   const graphData = {{ graph_json | safe }};
   const config = {{ config_json | safe }};

diff --git a/src/codegenome/templates/rules/cursor-rules.mdc b/src/codegenome/templates/rules/cursor-rules.mdc index 6796262..dab6019 100644 --- a/src/codegenome/templates/rules/cursor-rules.mdc +++ b/src/codegenome/templates/rules/cursor-rules.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/src/codegenome/templates/rules/markdown-instructions.md b/src/codegenome/templates/rules/markdown-instructions.md index 3666328..a959330 100644 --- a/src/codegenome/templates/rules/markdown-instructions.md +++ b/src/codegenome/templates/rules/markdown-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/src/codegenome/timeline.py b/src/codegenome/timeline.py index ed90f87..ca40d2c 100644 --- a/src/codegenome/timeline.py +++ b/src/codegenome/timeline.py @@ -1,4 +1,4 @@ -"""SQLite-backed graph snapshot and delta timeline for Watcher. +"""SQLite-backed graph snapshot and delta timeline for CodeGenome.

This module provides the GraphTimeline class, which records full dependency graphs into a SQLite database, allowing for historical analysis and diff --git a/test2.py b/test2.py new file mode 100644 index 0000000..fd1124c --- /dev/null +++ b/test2.py @@ -0,0 +1,13 @@ +import tree_sitter +import tree_sitter_python +lang = tree_sitter.Language(tree_sitter_python.language(), 'python') + +try:

  • p = tree_sitter.Parser()
  • p.set_language(lang)
  • print("set_language successful") +except AttributeError:
  • print("falling back to Parser(lang)")
  • p = tree_sitter.Parser(lang)

+print(p.parse(b'def foo(): pass')) diff --git a/tests/test_mcp_server.py b/tests/test_mcp_server.py index ff48133..8d9126f 100644 --- a/tests/test_mcp_server.py +++ b/tests/test_mcp_server.py @@ -1,4 +1,4 @@ -"""Tests for Watcher MCP server and graph store.""" +"""Tests for CodeGenome MCP server and graph store."""

from future import annotations