Resolve the graphify root marker when GRAPHIFY_OUT is shared and absolute

Update writes a raw, caller supplied watch path into the graphify_root
marker, which #777 deliberately chose over a resolved absolute so a
committed marker file stays portable across clones and CI runners.
That is fine as long as every reader of the marker runs with the same
CWD it was written from, which normally holds since the generated git
hooks and an unqualified graphify watch both assume it.

It stops holding once GRAPHIFY_OUT is set to an absolute, shared
location, the multi worktree setup from #686. The same marker file is
then reachable from any worktree's CWD, so a relative value like the
dot from graphify update dot resolves against whichever worktree
happens to read it later instead of the one that was actually
scanned, silently falling back to the wrong scan root.

Add a small helper that only resolves in that shared, absolute case
and otherwise keeps the existing relative behaviour untouched, so the
777 portability guarantee for the common, single clone case is
preserved rather than reverted.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_017qfdzgbA5KedGEjD1AayNh

graphify/watch.py

@@ -289,6 +289,30 @@ def _report_root_label(watch_path: Path) -> str:
     return Path.cwd().name if watch_path == Path(".") else str(watch_path)
 
 
+def _graphify_root_marker_value(watch_path: Path) -> str:
+    """The value to write into ``.graphify_root``.
+
+    Ordinarily preserves the caller-supplied path verbatim (relative or
+    absolute) so a committed ``graphify-out/.graphify_root`` stays portable
+    across clones and CI runners (#777): a relative marker like ``.`` is
+    meaningless outside the CWD it was written from, but every normal reader
+    of it (the generated git hooks, an unqualified ``graphify watch``) only
+    runs with that same CWD anyway.
+
+    That assumption breaks when ``GRAPHIFY_OUT`` itself is an absolute,
+    shared location (the multi-worktree / shared-output setup from #686):
+    the same marker file is then reachable from any worktree's CWD, not just
+    the one that wrote it, so a relative value silently resolves against
+    whichever worktree happens to be reading it instead of the one that was
+    actually scanned (#3375). Resolve to an absolute path in that case, since
+    portability across clones is not the goal there to begin with, the
+    output directory is already outside any one clone.
+    """
+    if Path(_GRAPHIFY_OUT).is_absolute():
+        return str(watch_path.resolve())
+    return str(watch_path)
+
+
 def _is_relative_to(path: Path, root: Path) -> bool:
     try:
         path.relative_to(root)
@@ -1950,9 +1974,13 @@ def _rebuild_code(
                 graph_tmp.write_text(candidate_graph_text, encoding="utf-8")
                 os_replace_with_fallback(graph_tmp, existing_graph)
 
-            # Write the user-supplied path only after the candidate graph is
-            # accepted, so a refused shrink cannot mismatch graph and marker.
-            (out / ".graphify_root").write_text(str(watch_path), encoding="utf-8")
+            # Write the scan root only after the candidate graph is accepted,
+            # so a refused shrink cannot mismatch graph and marker. See
+            # _graphify_root_marker_value for why this isn't always the raw
+            # caller-supplied value (#3375).
+            (out / ".graphify_root").write_text(
+                _graphify_root_marker_value(watch_path), encoding="utf-8"
+            )
 
             try:
                 from graphify.detect import save_manifest
@@ -2169,7 +2197,11 @@ def _rebuild_code(
             sig_file.write_text(
                 json.dumps({str(k): v for k, v in cur_sigs.items()}), encoding="utf-8")
 
-        (out / ".graphify_root").write_text(str(watch_path), encoding="utf-8")
+        # See _graphify_root_marker_value for why this isn't always the raw
+        # caller-supplied value (#3375).
+        (out / ".graphify_root").write_text(
+            _graphify_root_marker_value(watch_path), encoding="utf-8"
+        )
 
         try:
             from graphify.detect import save_manifest