[BUG] InstructionsLoaded hook does not fire for User and root Project CLAUDE.md at session start

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

The InstructionsLoaded hook does not fire for User CLAUDE.md (~/.claude/CLAUDE.md) or root Project CLAUDE.md at session start. It only fires for nested_traversal events (lazy loads when Claude reads files in subdirectories with their own CLAUDE.md).

The files are loaded into context — Claude can reference their contents when asked — but the hook simply never fires for them.

Expected Behavior

Per the docs, InstructionsLoaded should fire at session start for eagerly-loaded files with load_reason: "session_start". Events for User CLAUDE.md (memory_type: "User") and root Project CLAUDE.md (memory_type: "Project") should appear.

Actual Behavior

Only nested_traversal events fire. No session_start events are ever emitted.

Reproduction Steps

1. Create ~/.claude/CLAUDE.md with some content
2. Create a project with CLAUDE.md at root and a subdirectory apps/web/CLAUDE.md
3. Configure the InstructionsLoaded hook to log all events:

{
  "hooks": {
    "InstructionsLoaded": [
      {
        "hooks": [
          {
            "type": "command",
            "command": "cat >> /tmp/instructions-loaded.jsonl",
            "timeout": 5,
            "async": true
          }
        ]
      }
    ]
  }
}

1. Start a new Claude Code session in the project
2. Navigate into subdirectories so nested_traversal fires
3. Inspect /tmp/instructions-loaded.jsonl

Expected: Events with load_reason: "session_start" for User and root Project CLAUDE.md, plus nested_traversal for subdirectory CLAUDE.md files.

Actual: Only nested_traversal events appear. Example:

{"session_id":"23c82a42-...","load_reason":"nested_traversal","memory_type":"Project","file_path":"/path/to/apps/web/CLAUDE.md"}
{"session_id":"23c82a42-...","load_reason":"nested_traversal","memory_type":"Project","file_path":"/path/to/apps/web/src/components/CLAUDE.md"}

No events with load_reason: "session_start" are present.

Verification

• Confirmed the files are loaded into context (asked Claude to reference CLAUDE.md contents — it could)
• Checked both an OTLP pipeline (Loki) and a local JSONL audit log — both missing session_start events
• Other hooks (SubagentStart, SubagentStop, Notification, etc.) all work correctly
• The hook config has no matcher field (fires on all events per the docs)

Environment

• Claude Code version: 2.1.72
• OS: macOS (Darwin 25.2.0)
• Shell: zsh

Related Issues

• #30973 — InstructionsLoaded does not fire after compaction (different trigger, same hook)
• #31017 — InstructionsLoaded does not fire on /clear (different trigger, same hook)

Note: Both #30973 and #30897 show evidence that session_start events DO work for other users, suggesting this may be environment-specific or a regression.