deusdata--codebase-memory-mcp/docs/CONFIGURATION.md

# Configuration Reference

This page documents the configuration files that `codebase-memory-mcp` reads or writes today.

## At a Glance

| Purpose | Path | Format | Notes |
|---|---|---|---|
| Global custom extension mapping | `$XDG_CONFIG_HOME/codebase-memory-mcp/config.json` | JSON | Falls back to `~/.config/codebase-memory-mcp/config.json` when `XDG_CONFIG_HOME` is unset. |
| Per-project custom extension mapping | `{repo_root}/.codebase-memory.json` | JSON | Overrides conflicting global `extra_extensions` entries. |
| CLI-managed runtime settings | `${CBM_CACHE_DIR:-~/.cache/codebase-memory-mcp}/_config.db` | SQLite | Written by `codebase-memory-mcp config set/reset`. |
| UI settings | `${CBM_CACHE_DIR:-~/.cache/codebase-memory-mcp}/config.json` | JSON | Stores `ui_enabled` and `ui_port`. |
| Daemon operation log | `${CBM_CACHE_DIR:-~/.cache/codebase-memory-mcp}/logs/cbm-daemon.log` | Structured log | Durable daemon lifecycle, watcher/indexing, UI, resource, and error events. |
| Admission conflict log | `${CBM_CACHE_DIR:-~/.cache/codebase-memory-mcp}/logs/daemon-conflicts.ndjson` | NDJSON | Exact-build, ABI, and canonical-cache conflicts. |
| Activation log | `${CBM_CACHE_DIR:-~/.cache/codebase-memory-mcp}/logs/activation-events.ndjson` | NDJSON | Install/update/uninstall activation progress and outcomes. |

CBM resolves `CBM_CACHE_DIR` to a canonical per-account path before using any of these locations. The log directory and files are private to the account.

## 1. Custom File Extension Mapping

Two optional JSON files let you map additional file extensions to built-in languages.

### Global config

Default path:

```text
$XDG_CONFIG_HOME/codebase-memory-mcp/config.json
```

Fallback when `XDG_CONFIG_HOME` is unset:

```text
~/.config/codebase-memory-mcp/config.json
```

### Per-project config

Place this file in the repository root:

```text
.codebase-memory.json
```

### Format

```json
{
  "extra_extensions": {
    ".blade.php": "php",
    ".mjs": "javascript",
    ".twig": "html"
  }
}
```

Notes:

- Extension keys must include the leading dot.
- Language names are case-insensitive.
- Unknown language names are skipped.
- Missing files are ignored.
- If the same extension appears in both files, the per-project file wins.

## 2. CLI-Managed Runtime Settings

The `config` subcommand stores runtime settings in a small SQLite database:

```text
${CBM_CACHE_DIR:-~/.cache/codebase-memory-mcp}/_config.db
```

Inspect or change values with the CLI:

```bash
codebase-memory-mcp config list
codebase-memory-mcp config get auto_index
codebase-memory-mcp config set auto_index true
codebase-memory-mcp config set auto_index_limit 50000
codebase-memory-mcp config reset auto_index
```

Current keys:

| Key | Default | Meaning |
|---|---|---|
| `auto_index` | `false` | Automatically index new projects when an MCP session starts. |
| `auto_index_limit` | `50000` | Maximum file count allowed for automatic indexing of a new project. |

## 3. UI Settings

The optional built-in graph UI stores its settings in:

```text
${CBM_CACHE_DIR:-~/.cache/codebase-memory-mcp}/config.json
```

Current format:

```json
{
  "ui_enabled": false,
  "ui_port": 9749
}
```

Notes:

- If a UI-enabled binary finds its verified external asset pack and no UI config file exists yet, the UI auto-enables on first run. Missing or invalid assets leave the MCP/daemon service available and keep the UI disabled.
- `CBM_CACHE_DIR` changes both the UI config location and the runtime settings database location.
- CBM resolves `CBM_CACHE_DIR` to one canonical per-account cache root. A process configured with a different root fails while any CBM session or command is active; close them before switching roots.

## 4. Environment Variables

These environment variables affect runtime behavior:

| Variable | Default | Description |
|---|---|---|
| `CBM_ALLOWED_ROOT` | *(unset)* | Confine `index_repository` to paths within this directory. When set, a `repo_path` that resolves (after symlink / `..` resolution) outside this root is refused, and the same check now applies to the graph UI's `POST /api/index` route rather than only to the MCP tool. Unset imposes no *containment* restriction — but see the always-on limits below, which apply whether or not this is set. Useful when the server may be driven by an untrusted caller, e.g. agentic or multi-tenant deployments. |
| `CBM_CACHE_DIR` | `~/.cache/codebase-memory-mcp` | Override the cache directory used for indexes, `_config.db`, and UI `config.json`. |
| `CBM_DIAGNOSTICS` | `false` | Enable periodic `snapshot.json` and retained `trajectory.ndjson` below a fresh owner-private directory in the system temp directory. The daemon records the randomized paths in the `diagnostics.start` discovery record (a single JSON line) in `${CBM_CACHE_DIR}/logs/cbm-daemon.log`; that one record is emitted even when `CBM_LOG_LEVEL` suppresses ordinary logging, so the paths always remain discoverable. |
| `CBM_DOWNLOAD_URL` | GitHub releases | Override the update download URL. |
| `CBM_LOG_LEVEL` | `info` | Set the log level to `debug`, `info`, `warn`, `error`, or `none` (or `0`-`4`). Thin-frontend messages use that session's stderr; detached daemon events use `${CBM_CACHE_DIR}/logs/cbm-daemon.log`. |
| `CBM_WORKERS` | auto-detected | Override the indexing worker count. |

Environment used by daemon-owned components—such as diagnostics, daemon logging, and process-wide indexing resource limits—is captured from the first daemon-backed session that starts the daemon. Later sessions join the existing process and cannot replace those values. To change them, close every daemon-backed session, update the relevant agent configurations consistently, and restart a session. `CBM_ALLOWED_ROOT` remains session-specific, a conflicting `CBM_CACHE_DIR` is rejected, and one-shot CLI commands use their own current environment without starting the daemon.


### Roots that are always refused

Independently of `CBM_ALLOWED_ROOT`, some directories are refused as an indexing
root because they are too broad or too sensitive to index as a unit:

- a filesystem root, a Windows drive root, or a UNC share root;
- a top-level system tree — `/etc`, `/var`, `/usr`, `/home`, `/Users`, and on
  Windows `C:\Windows`, `C:\Users`, `C:\ProgramData`, `C:\Program Files`;
- your home directory itself (directories *below* it are fine);
- a credential directory at any depth — `.ssh`, `.aws`, `.gnupg`, `.kube`,
  `.docker`, `.netrc`, `.git-credentials`, `.password-store`, macOS `Keychains`.

Two limits are worth stating plainly. This constrains *scope*, not
*sensitivity*: inside a root that is allowed, every file the process can read may
be indexed and later returned. And the credential list is a denylist, so it
raises the cost of a mistake rather than closing the class — a directory it does
not name is permitted.

## 5. Agent and Editor Integration Files

The `install` command can also write MCP entries and instruction blocks into agent/editor config files such as Claude Code, Codex, Gemini, VS Code, Cursor, Zed, and others.

Those target paths vary by tool and platform, so the easiest way to inspect the exact files for your machine is:

```bash
codebase-memory-mcp install --dry-run
```

That prints the specific config files the installer would modify without writing anything.