fix(manifest): clear recovered marker on managed re-record + reject '..' in is_recovered

Address Copilot Round-7 review comments on PR #2483:

1. record_existing(recovered=False) and record_file now BOTH discard the
   path from _recovered_files. The marker is meant to flag "we observed
   this file but cannot vouch it's a managed baseline" — once the same
   path is re-recorded as managed (either explicitly or by writing fresh
   bytes), the marker is stale and must clear so refresh_managed and
   future is_recovered queries return the truthful answer.

2. is_recovered now applies the same canonical-key guard as record_existing
   (rejects absolute paths and '..' segments lexically before delegating
   to _validate_rel_path). Such paths can never be stored keys, so the
   query correctly returns False without depending on _validate_rel_path
   semantics that diverged from record_existing's stricter contract.

record_file docstring updated to mention the side-effect on recovered
markers.

Tests: 3 new methods in TestManifestRecoveredFiles covering
record_existing(false) clearing, record_file clearing, and is_recovered
dotdot rejection.

src/specify_cli/integrations/manifest.py

@@ -132,6 +132,9 @@ class IntegrationManifest:
 
         Creates parent directories as needed.  Returns the absolute path
         of the written file.
+        If the path was previously marked as recovered via
+        ``record_existing(recovered=True)``, the recovered marker is
+        cleared because the bytes are now produced, not merely observed.
 
         Raises ``ValueError`` if *rel_path* resolves outside the project root.
         """
@@ -145,6 +148,9 @@ class IntegrationManifest:
 
         normalized = abs_path.relative_to(self.project_root).as_posix()
         self._files[normalized] = hashlib.sha256(content).hexdigest()
+        # ``record_file`` writes *produced* content, so any prior
+        # recovered marker for this path is no longer accurate.
+        self._recovered_files.discard(normalized)
         return abs_path
 
     def record_existing(self, rel_path: str | Path, *, recovered: bool = False) -> None:
@@ -201,6 +207,12 @@ class IntegrationManifest:
         self._files[normalized] = _sha256(abs_path)
         if recovered:
             self._recovered_files.add(normalized)
+        else:
+            # ``recovered=False`` means the caller is asserting this path is
+            # managed-baseline now, not merely observed; drop any stale
+            # recovered marker so future is_recovered() queries reflect the
+            # transition. ``discard`` is a no-op when the key is absent.
+            self._recovered_files.discard(normalized)
 
     # -- Querying ---------------------------------------------------------
 
@@ -224,15 +236,17 @@ class IntegrationManifest:
     def is_recovered(self, rel_path: str | Path) -> bool:
         """Return True if *rel_path* was recorded via ``record_existing(recovered=True)``.
 
-        Input is normalized through the same ``_validate_rel_path`` pipeline that
-        ``record_existing`` uses for its stored keys, so the two methods agree
-        on key format. Absolute paths and paths that escape the project root
-        return ``False`` (they cannot match the relative POSIX keys we store) —
-        consistent with Python's membership-predicate convention of not raising
-        on a not-in-set query.
+        Input is normalized through the same pipeline as ``record_existing``:
+        absolute paths, paths escaping the project root, AND paths containing
+        ``'..'`` segments are rejected (returned as ``False``). This mirrors
+        ``record_existing``'s canonicalization guard — such paths can never
+        appear as stored keys, so the answer is always ``False``.
         """
+        rel = Path(rel_path)
+        if rel.is_absolute() or ".." in rel.parts:
+            return False
         try:
-            abs_path = _validate_rel_path(Path(rel_path), self.project_root)
+            abs_path = _validate_rel_path(rel, self.project_root)
             normalized = abs_path.relative_to(self.project_root).as_posix()
         except ValueError:
             return False

tests/integrations/test_manifest.py

@@ -375,6 +375,37 @@ class TestManifestRecoveredFiles:
         # Don't record anything — the path is impossible to record anyway.
         assert m.is_recovered("../escape.txt") is False
 
+    def test_record_existing_clears_recovered_when_false(self, tmp_path):
+        # Finding A: re-recording the same path with recovered=False must
+        # drop the prior recovered marker (transition to managed baseline).
+        f = tmp_path / "x.txt"
+        f.write_text("v1", encoding="utf-8")
+        m = IntegrationManifest("test", tmp_path)
+        m.record_existing("x.txt", recovered=True)
+        assert m.is_recovered("x.txt") is True
+        m.record_existing("x.txt", recovered=False)
+        assert m.is_recovered("x.txt") is False
+
+    def test_record_file_clears_recovered(self, tmp_path):
+        # Finding A: record_file writes produced content; the path can no
+        # longer be considered "merely observed" once we wrote bytes.
+        (tmp_path / "y.txt").write_text("observed", encoding="utf-8")
+        m = IntegrationManifest("test", tmp_path)
+        m.record_existing("y.txt", recovered=True)
+        assert m.is_recovered("y.txt") is True
+        m.record_file("y.txt", "produced")
+        assert m.is_recovered("y.txt") is False
+
+    def test_is_recovered_rejects_dotdot_segment(self, tmp_path):
+        # Finding B: record_existing rejects ``..`` segments via the lexical
+        # pre-check; is_recovered must match that behavior and return False
+        # without raising, mirroring the canonicalization guard.
+        (tmp_path / "z.txt").write_text("v1", encoding="utf-8")
+        m = IntegrationManifest("test", tmp_path)
+        m.record_existing("z.txt", recovered=True)
+        # Same file via dotdot-normalizing path — must be False, not raise.
+        assert m.is_recovered("subdir/../z.txt") is False
+
 
 class TestRecordExistingNewGuards:
     """Coverage for the two new guards added by Copilot's 2026-05-18 review."""