Shadow branches contain corrupted tree objects with empty filenames on Windows

[RobertIsho]

Bug Summary

Entire CLI creates shadow branches (entire/<commit>-<hash>) containing git tree objects with empty filename entries. This corrupts the git repository — git fsck reports badTree errors and git bundle create --all fails.

Environment

• OS: Windows 10 Home 10.0.19045
• Entire CLI: dev (unknown) — Go 1.26.1, windows/amd64
• Git: 2.52.0.windows.1
• Repo path: C:\Users\rober\Vaults\Flowsign (an Obsidian vault)

Root Cause

Entire CLI appears to be splitting the absolute Windows repo path (C:\Users\rober\Vaults\Flowsign) into tree entries by path component. The drive letter C: gets split into:

1. An empty-named directory entry (the part before C)
2. A directory named c
3. A directory named Users
4. ...and so on

The empty-named entry (entry #1) is invalid per git's tree object format. Git requires all tree entries to have non-empty filenames.

Reproduction

# 1. Check for corrupted trees
git fsck --full 2>&1 | grep "badTree" | wc -l
# Output: 34

# 2. Show the corruption
git fsck --full 2>&1 | head -4
# error: empty filename in tree entry
# error: empty filename in tree entry
# error in tree 0f996a098e26ad70bb4a8b0cc367c3c0b92193a8: badTree: cannot be parsed as a tree

# 3. Examine a corrupted tree (raw binary parse)
# Entry 6 in tree 0f996a09... has mode=40000, name="" (empty string)
# That empty-named tree contains: "" -> c -> Users -> rober -> ...
# This is the absolute Windows path leaking into the tree structure

# 4. Show what the empty-named tree resolves to
git cat-file -p 80de0046f62591d42e08b1e4ff700c19ec6a9c3e
# 040000 tree 5c1b42b451dd51d91a21e08ca06630e94851a17b    c

git cat-file -p 5c1b42b451dd51d91a21e08ca06630e94851a17b
# 040000 tree f0fcfbc3b7d45c637a1a01d4152e5840e1bd87fb    Users

git cat-file -p f0fcfbc3b7d45c637a1a01d4152e5840e1bd87fb
# 040000 tree 23f90b8d9004a854a59ef2b66da74005afd70569    rober

# 5. This breaks git bundle (used by tools like Claude Code /ultraplan)
git bundle create /tmp/test.bundle --all
# fatal: empty filename in tree entry
# error: pack-objects died

# 6. Main branch alone bundles fine — corruption is only in entire/* branches
git bundle create /tmp/test.bundle main
# (succeeds)

Impact

• 34 corrupted tree objects across 280 shadow branches
• git bundle create --all fails completely — blocks any tool that needs to pack the full repo
• git fsck reports errors on every run
• entire clean --force removes the shadow branches but the corrupted tree objects remain in the object store until garbage collected

Workaround

entire clean --force    # removes 280 shadow branches
git gc --prune=now      # removes unreferenced corrupted objects

Expected Behavior

Shadow branch tree objects should only contain paths relative to the repository root, not absolute Windows paths. The drive letter component (C:) should never appear in tree entries.

Additional Context

• All 280 shadow branches follow the entire/<short-sha>-e3b0c4 naming pattern
• The entire/checkpoints/v1 branch and main branch are NOT corrupted
• The corruption is consistent: every shadow branch has the same empty-filename tree entry at the same position (entry 6 in the root tree)
• entire clean correctly identifies these as orphaned shadow branches