newTrack writes spec.md, plan.md, metadata.json and index.md to conductor folder

[richardaskham]

For some reason newTrack has started writing spec and plan files to the incorrect location. Instead of writing to the conductor/tracks/ folder, :newTrack writes spec.md, plan.md, metadata.json and index.md to conductor folder. This also overwrites the index.md file in the conductor folder. It then detects the issue, and needs to restore index.md from git, and try again. It now does this consistently on every newTrack I add

[piero-94]

Same problem here. I believe the cause is in the newTrack.toml file, line 8:

PLAN MODE PROTOCOL: Parts of this process run within Plan Mode. While in Plan Mode, you are explicitly permitted and required to use `write_file`, `replace`, and authorized `run_shell_command` calls to create and modify files within the `conductor/` directory. **CRITICAL: You MUST use relative paths starting with `conductor/` (e.g., `conductor/product.md`) for all file operations. Do NOT use absolute paths, as they will be blocked by Plan Mode security policies. REDIRECTION (e.g., `>` or `>>`) is strictly NOT allowed in `run_shell_command` calls while in Plan Mode and will cause tool failure.**

On Windows, this forced behavior leads to malformed paths of the form conductor/tracks/trackname/spec.md, which are evaluated by Gemini as conductor/spec.md.

[callorange]

[Bug Report] Plan Mode Path Flattening in write_file

Root Cause Identified: Gemini CLI Plan Mode Path Flattening Bug

I have identified that the issue where newTrack fails to create artifacts in the correct subdirectories is caused by a core platform bug in the Gemini CLI sandbox engine.

1. Issue Summary

During Plan Mode, the write_file tool flattens nested relative paths, stripping all intermediate directories (e.g., conductor/tracks/<track_id>/index.md becomes conductor/index.md). This results in the silent overwriting of the project's root index.md and corrupts the intended track structure.

2. Official Bug Report

I have submitted a formal bug report to the Gemini CLI repository here:
google-gemini/gemini-cli#25131

3. CRITICAL RECOMMENDATION for Users

Until this platform-level bug is resolved, the newTrack command is effectively broken for nested structures in Plan Mode. I strongly advise users to NOT use Plan Mode during track initialization.

By executing newTrack in Default/Normal Mode, the path resolution works correctly and all artifacts are created in their designated subdirectories without flattening.

4. Manual Workaround (if already corrupted)

If you have already run newTrack in Plan Mode and your project root is corrupted, please:

1. Restore the accidentally overwritten conductor/index.md.
2. Manually move the flattened track artifacts from the root conductor/ directory into the intended conductor/tracks/<track_id>/ subdirectory.

5. Technical Analysis

This appears to be a logic flaw in the core sandbox engine's path normalization during Plan Mode. The full path correctly matches the security policy's argsPattern, but it is truncated during the actual I/O operation. This issue is exclusive to Plan Mode and does NOT occur in Default/Normal Mode.

I hope the Gemini CLI team addresses this issue promptly so that the conductor framework's automation logic can function as designed in Plan Mode.