[BUG] Ultraplan CCR session fails to read tracked files — path resolution mismatch in cloud environment

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 running /ultraplan from a clean, fully-pushed git repository, the CCR cloud session fails to read files that verifiably exist on the remote branch. The planning agent attempts to access a file at /home/user/navsim/planning/script/config/common/agent/SafeDrive_2stage_GeoBEV_newbase_motionAnchorCls.yaml but reports "File does not exist", with the working directory shown as /home/user.
All of the following have been confirmed locally:

git rev-parse --show-toplevel correctly returns the repo root
git status shows clean working tree, up to date with origin/main
git ls-files confirms the file is tracked
git log origin/main confirms the file exists on the remote
git check-ignore confirms the file is not gitignored
No submodules are involved (.gitmodules does not exist)
The file is visible on GitHub web UI

The repo root is correct, there are no nested or ancestor git repos, and the file is present on the remote — yet the CCR session cannot access it.

What Should Happen?

The CCR cloud session should correctly clone the repository and resolve file paths so that all git-tracked files are readable by the planning agent.

Error Messages/Logs

Read /home/user/navsim/planning/script/config/common/agent/SafeDrive_2stage_GeoBEV_newbase_motionAnchorCls.yaml
File does not exist. Note: your current working directory is /home/user.

Steps to Reproduce

Steps to Reproduce

1. Have a GitHub-hosted repository with files committed and pushed to origin/main
2. Confirm the repo is clean and in sync:

'''
$ git rev-parse --show-toplevel
/home/jiyong/Jiyong/navsim_e2e/safedrive_adr

$ git branch --show-current
main

$ git status
On branch main
Your branch is up to date with 'origin/main'.
nothing to commit, working tree clean

$ git log origin/main..HEAD --oneline
(empty)
'''

1. Confirm the target file is tracked and present on the remote:

'''
$ git ls-files navsim/planning/script/config/common/agent/SafeDrive_2stage_GeoBEV_newbase_motionAnchorCls.yaml
navsim/planning/script/config/common/agent/SafeDrive_2stage_GeoBEV_newbase_motionAnchorCls.yaml

$ git log origin/main --oneline -1 -- navsim/planning/script/config/common/agent/SafeDrive_2stage_GeoBEV_newbase_motionAnchorCls.yaml
865c587 Update yaml

$ git check-ignore -v navsim/planning/script/config/common/agent/SafeDrive_2stage_GeoBEV_newbase_motionAnchorCls.yaml
(empty — not ignored)
'''

1. Confirm no submodules:

'''
$ cat .gitmodules
cat: .gitmodules: No such file or directory

$ git submodule status
(empty)
'''

1. Confirm the file is visible on GitHub web UI
2. Run /ultraplan <prompt> from the repo root
3. The cloud planning agent fails to read the file with the error above

Claude Model

Opus

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.1.107

Platform

Anthropic API

Operating System

Ubuntu/Debian Linux

Terminal/Shell

Other

Additional Information

Repo type: Private, GitHub-hosted
No nested git repos: No .git directory exists in any ancestor path above the repo root
No submodules

The error path /home/user/navsim/... suggests the CCR environment may have cloned the repo into /home/user/ but the model is not prefixing the repo directory name when constructing file paths, or the repo contents were extracted at the wrong level.
Possibly related issues:

#44643 — Remote session (ultraplan) receives wrong project context
#44815 — /ultraplan always routes to wrong workspace, plan agent gets no context
#46302 — /ultraplan attaches to ancestor git repository, ignoring nested repo in CWD

This issue differs from the above: the git repo root is correctly identified, there are no nested/ancestor repos involved, and the file is confirmed on the remote. The problem appears to be specifically in how the CCR environment resolves file paths after cloning.
Ultraplan session URL: https://claude.ai/code/session_01E2Y1s1kmRBdicCx8e78s8A