CodeGraph writes .git/info/exclude when .git exists but is not a valid repository

[XucroYuri]

Summary

The bundled CodeGraph SessionStart helper writes .git/info/exclude whenever a .git path exists, even when that path is an empty or otherwise invalid repository marker. On Windows, Codex can leave such invalid .git directories behind; CodeGraph then mutates them into a more persistent partial Git structure, which combines badly with Codex Desktop's repeated Git discovery.

Environment

• LazyCodex installed: 4.16.2
• Latest LazyCodex source checked: bb8764ca1754148ca56478d433c42b91c550e0f4 (main)
• Codex Desktop: 26.707.3748.0
• Codex CLI: 0.144.1
• OS: Windows 11 Pro for Workstations, build 26200, x64
• Relevant config: OMO CodeGraph MCP and SessionStart hook enabled

Repository Decision

• Target repository: code-yeongyu/lazycodex
• Why this belongs here: the invalid-repository write occurs in the bundled OMO CodeGraph integration, not in upstream Codex Git discovery.
• LazyCodex evidence: latest plugins/omo/components/codegraph/dist/cli.js, lines 307-325, contains ensureCodegraphGitignored(). It checks only existsSync(workspace/.git), recursively creates .git/info, and appends .codegraph to exclude.
• Upstream Codex evidence: Windows sandbox helper creates an empty .git directory for a nonexistent deny-write path, triggering repeated Git probes and high Defender CPU usage openai/codex#32324 documents a Windows sandbox path that can create an empty .git marker. CodeGraph should still treat that as invalid input and avoid mutating it.

Reproduction

1. Create a normal non-Git workspace.
2. Create an empty .git directory in it, matching the invalid marker produced by the Windows sandbox report.
3. Run the LazyCodex CodeGraph SessionStart bootstrap for that workspace.
4. Inspect .git/info/exclude and run git -C <workspace> rev-parse --is-inside-work-tree.

Minimal state before the hook:

workspace/
  .git/        # empty, not a repository

Observed state after the hook:

workspace/
  .git/
    info/
      exclude  # contains .codegraph

git rev-parse --is-inside-work-tree still fails because the workspace is not a repository.

Expected Behavior

CodeGraph must leave an invalid .git path untouched. It should write an exclude entry only after Git confirms that the workspace is a valid worktree and resolves the correct per-worktree exclude path.

Actual Behavior

ensureCodegraphGitignored() treats existence as validity:

const gitDir = join(workspace, ".git");
if (!existsSync(gitDir)) return false;
const excludePath = join(gitDir, "info", "exclude");
mkdirSync(join(gitDir, "info"), { recursive: true });
appendFileSync(excludePath, ".codegraph\n");

On the affected machine, D:\TTS\.git was created at 10:17:14 as an invalid marker. At 17:27:30, after CodeGraph startup, its only content became .git/info/exclude with the 11-byte value .codegraph\n. The top-level .git creation predates the CodeGraph write, so CodeGraph did not create the marker but did mutate and preserve the invalid structure.

Evidence

• Latest bundled implementation: plugins/omo/components/codegraph/dist/cli.js:307-325 at bb8764ca1754148ca56478d433c42b91c550e0f4.
• Runtime filesystem state: invalid D:\TTS\.git; only .git/info/exclude; exact bytes 2e 63 6f 64 65 67 72 61 70 68 0a (.codegraph\n).
• git -C D:\TTS rev-parse --is-inside-work-tree fails.
• Adjacent upstream report: Windows sandbox helper creates an empty .git directory for a nonexistent deny-write path, triggering repeated Git probes and high Defender CPU usage openai/codex#32324

Root Cause

Repository validity is reduced to existsSync(<workspace>/.git). This does not distinguish a valid repository from an empty sandbox-created directory, and it does not handle linked worktrees where .git is a file. The helper then creates repository-internal paths before Git has validated or resolved them.

Proposed Fix

1. Ask Git to validate and resolve the path, for example with a bounded git -C <workspace> rev-parse --git-path info/exclude after confirming --is-inside-work-tree.
2. Do not call mkdirSync or appendFileSync when validation fails.
3. Use the Git-resolved exclude path so linked worktrees are handled correctly.
4. Add regression tests for an empty .git directory, a normal repository, and a linked worktree whose .git is a file.

Verification Plan

• Given an empty .git, the hook returns a skipped/not-repository result and leaves the filesystem unchanged.
• Given a valid repository, .codegraph is added once to the Git-resolved exclude file.
• Given a linked worktree, the exclude entry is written to the correct common/worktree Git path without replacing the .git file.
• Re-running SessionStart remains idempotent.

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This issue or PR was generated by LazyCodex.
Tag: lazycodex-generated