fix(cli): resolve the graph from the primary checkout in linked worktrees (#2008)

[HerenderKumar]

Summary

Fixes #2008. The read commands (query / explain / path / affected) resolve their default graph to <GRAPHIFY_OUT>/graph.json relative to CWD. Run from a linked git worktree — increasingly the default for AI-agent task isolation (Claude Code etc.) — that path does not exist, so the command fails hard with Graph file not found and callers have to wrap every invocation in a git rev-parse --git-common-dir shim.

Fix

cli.py::_default_graph_path() — used only by the read commands; writers resolve through graphify.paths — gains a worktree fallback: when the local graph is absent and CWD is inside a linked worktree (--git-dir != --git-common-dir, the same absolute compare the commit/post-checkout hooks already use for #1809), resolve to the primary checkout's graph.

Read-only and surgical by construction:

• writers (extract / build) never touch this helper — a write is never redirected;
• an explicit --graph still overrides;
• an absolute GRAPHIFY_OUT short-circuits (already shared across worktrees);
• an absent primary graph keeps the original "run extract" error;
• the two git rev-parse probes run only on the cold path (no local graph), so the common case is untouched.

Testing

New tests/test_worktree_graph_path.py (real git worktree, no grammar deps):

• resolves the primary checkout's graph from a linked worktree (red→green verified against origin/v8);
• a worktree that built its own graph keeps using it (local wins);
• the primary checkout is unaffected (local default preserved);
• outside a git repo the resolver never raises.

tests/test_explain_cli.py + tests/test_affected_cli.py pass unchanged.

[IskandarovFirdavs]

Nice helper function. Would it be worth adding a short docstring explaining why graph.json is the default output path?

[HerenderKumar]

Thanks !!! Actually both new functions already carry docstrings, If I mention specifically _default_graph_path (lines 85–93) and _worktree_primary_graph (lines 104–113). _default_graph_path explains why <GRAPHIFY_OUT>/graph.json is the default and how the worktree fallback kicks in, and _worktree_primary_graph documents the git-dir vs. git-common-dir check and every case where it returns None. Btw I am happy to extend further if any part seems less explanatory.

[IskandarovFirdavs]

Using Path here improves readability. Is there any scenario where _GRAPHIFY_OUT could be missing or invalid? If so, should that be handled explicitly?

[HerenderKumar]

Thanks !!! Agreed on Path. On _GRAPHIFY_OUT — it isn't a value that gets passed in while the program runs. It's a fixed setting loaded once at the top of the file (line 14), so it's always a valid string (defaults to graphify-out). If it were ever wrong, the program wouldn't even start — it'd fail right at import, not inside this function. The only tricky case is when it's set to an absolute path, and that's already handled at line 114 (the os.path.isabs check). So there's nothing extra to handle here. That said, I'm happy to add a check if you'd still like one just to be safe.