fix(paths): handle submodule gitdirs in worktree IDs

[MuskanPaliwal]

Fixes #640.

This fixes session initialization in repositories that contain Git submodules. GetWorktreeID previously treated any .git file whose gitdir: target did not contain .git/worktrees/<id> or .bare/worktrees/<id> as invalid. Ordinary submodules use a different valid Git layout: their checkout has a .git file pointing into the parent repository .git/modules/... directory. That caused Entire to fail before a session could initialize with unexpected gitdir format (no worktrees).

Core Changes:

• Teach GetWorktreeID to recognize ordinary submodule gitdirs under .git/modules/<submodule> and return an empty worktree ID for them.
• Keep linked-worktree behavior unchanged for regular worktrees under .git/worktrees/<id> and bare-worktree layouts under .bare/worktrees/<id>.
• Add explicit parsing for submodule-owned linked worktrees, where the gitdir is shaped like .git/modules/<submodule>/worktrees/<id>.
• Avoid misattributing a parent repository worktree ID to a submodule. A gitdir like .git/worktrees/<parent-worktree>/modules/<submodule> means the parent repo is a linked worktree, but the submodule itself is still an ordinary submodule checkout, so the returned submodule worktree ID should be empty.
• Split the gitdir parsing into parseWorktreeID so the shape-specific logic is isolated and covered by focused tests.
• Add regression coverage for relative submodule gitdirs, absolute submodule gitdirs, nested submodules, submodules inside linked superproject worktrees, and linked worktrees of submodules.

API Notes:

• No public CLI command or flag changes.
• No user-facing output changes except avoiding the erroneous session-initialization failure for valid submodule checkouts.
• The GetWorktreeID contract remains: return an empty string for the main checkout namespace, return a non-empty ID for a real linked worktree namespace, and return an error for unrecognized .git file formats.

Compatibility / Release Notes:

• Breaking changes: None.
• Version impact: None.
• Rollout notes: Existing repositories need no migration. The change only broadens accepted Git metadata layouts for session initialization.
• E2E tests were not run; this PR is covered by focused paths package regression tests and a manual local submodule smoke check.

Validation:

• GOCACHE=/private/tmp/entire-go-cache go test ./cmd/entire/cli/paths -run ^TestGetWorktreeID$ -count=1 passed.
• git diff --check upstream/main...HEAD passed.
• Manual local submodule smoke check confirmed Git writes gitdir: ../../.git/modules/deps/lib for a real submodule checkout, matching the issue layout.

[MuskanPaliwal]

Hi @blackgirlbytes , can I get a review on this PR ?

[claude]

Claude Code Review

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