Graphify Codex install does not reliably make the agent use Graphify first for orientation due to the graph files being dirty in workspace #860

Description

I have Graphify installed for Codex with both AGENTS.md configured and the .codex/hooks.json PreToolUse hook registered. The install reports success and says Codex will check the knowledge graph before answering codebase questions and rebuild it after code changes.

In practice, the agent still skipped Graphify and went straight to targeted local rg / file inspection during a normal code-change task where Graphify should have been the first orientation step.

The main reason it gave was that graphify-out/ files were dirty in the git worktree, even though those files are expected to change frequently and may often be dirty because of Graphify’s update flow and hooks.

The issue is that the current Codex integration does not make it reliable enough that the agent will still use Graphify first when graphify-out/ is present but dirty.

Observed Behavior

• graphify codex install reports successful setup
• AGENTS.md is configured
• .codex/hooks.json has the PreToolUse hook
• despite that, Codex may still bypass Graphify and inspect files directly first
• in this case, the agent treated dirty graphify-out/ files as a reason not to use Graphify for orientation

Expected Behavior

When graphify-out/ exists, Codex should still reliably use Graphify as the default orientation step before broad search or multi-file inspection, even if graphify-out/ is dirty.

Dirty graph artifacts should not be treated as a reason to skip Graphify unless the task is specifically about stale or incorrect graph output, or the user has said not to rely on it.