[BUG] nested_traversal re-injects same CLAUDE.md into context on every file access in that directory

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?

When Claude Code reads a file in a subdirectory that has its own CLAUDE.md, the nested_traversal mechanism re-injects the same CLAUDE.md into the context window every time — even if it was already loaded earlier in the session. There is no deduplication.

This wastes context window capacity with redundant instruction content.

Evidence

I captured OTEL telemetry (api_request events with token counts) alongside InstructionsLoaded hook events for a single session. The data clearly shows context jumps each time the same CLAUDE.md is re-loaded.

Session: f3736323-1a26-460f-9dc9-845ee0c4c9b6

InstructionsLoaded events (same file loaded 3 times):

| Time | memory_type | load_reason | file_path |
|------|-------------|-------------|-----------|
| 03:52:12 | Project | nested_traversal | .../apps/web/CLAUDE.md |
| 04:03:57 | Project | nested_traversal | .../apps/web/CLAUDE.md |
| 04:04:14 | Project | nested_traversal | .../apps/web/CLAUDE.md |

Token counts from api_request OTEL events:

Time      total_context_tokens
03:52:10  26,973   ← before first load of apps/web/CLAUDE.md
03:52:17  45,593   ← after first load (+18,620 tokens)

The same ~18k-token CLAUDE.md was injected into context 3 times during this session.

Expected Behavior

Once a CLAUDE.md file has been loaded via nested_traversal in a session, subsequent accesses to files in the same directory should not re-inject the same instruction content into context. Claude Code should deduplicate already-loaded instruction files.

Actual Behavior

Every file read that triggers nested_traversal re-injects the full content of the directory's CLAUDE.md, even if it was already loaded earlier in the same session. This causes unnecessary context window consumption.

Reproduction Steps

1. Create a project with a large CLAUDE.md in a subdirectory (e.g., apps/web/CLAUDE.md)
2. Enable OTEL telemetry to capture api_request token counts
3. Configure InstructionsLoaded hook to log events
4. Start a session and ask Claude to read multiple files under apps/web/
5. Observe that InstructionsLoaded fires for apps/web/CLAUDE.md on each file access
6. Observe that total_context_tokens jumps by the same amount each time

Impact

• Wastes context window budget (the scarcest resource in long sessions)
• Larger CLAUDE.md files amplify the waste
• Monorepos with many subdirectory CLAUDE.md files are especially affected

Environment

• Claude Code version: 2.1.72
• OS: macOS Darwin 25.2.0