feat(directory): CODEGRAPH_DIR env var to override the index dir name (#636) (#741)

Two environments that share one working tree — most concretely Windows
and WSL — can't safely share a single `.codegraph/`: the daemon lockfile
records a platform-specific pid + socket (named pipe vs Unix socket), and
SQLite locking across the WSL2/Windows filesystem boundary is unreliable,
so two daemons over one index risks corruption.

Add a `CODEGRAPH_DIR` env var (default `.codegraph`) that overrides the
per-project data directory name, so each environment keeps its own index
in the same tree (e.g. `CODEGRAPH_DIR=.codegraph-win` on Windows). The
name is resolved live and validated (rejects separators / `..` / absolute,
falling back to the default with a one-time stderr warning). Indexing and
file-watching now skip ANY `.codegraph-*` sibling so neither side trips
over the other's data.

Routes the previously-hardcoded `.codegraph` literals (db path, lockfile,
error log, watcher ignore, file-scan skip, installer) through the
resolver. No extraction-version bump — index content is unchanged.

Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

src/extraction/index.ts

@@ -18,6 +18,7 @@ import {
 import { QueryBuilder } from '../db/queries';
 import { extractFromSource } from './tree-sitter';
 import { detectLanguage, isSourceFile, isLanguageSupported, isFileLevelOnlyLanguage, initGrammars, loadGrammarsForLanguages } from './grammars';
+import { isCodeGraphDataDir } from '../directory';
 import { logDebug, logWarn } from '../errors';
 import { validatePathWithinRoot, normalizePath } from '../utils';
 import ignore, { Ignore } from 'ignore';
@@ -454,8 +455,9 @@ function scanDirectoryWalk(
     }
 
     for (const entry of entries) {
-      // Never descend into git internals or our own data directory.
-      if (entry.name === '.git' || entry.name === '.codegraph') continue;
+      // Never descend into git internals or any CodeGraph data directory
+      // (the active one or a sibling another environment created — #636).
+      if (entry.name === '.git' || isCodeGraphDataDir(entry.name)) continue;
 
       const fullPath = path.join(dir, entry.name);
       const relativePath = normalizePath(path.relative(rootDir, fullPath));