fix(presets): recompose surviving skills when a lower preset layer is removed

src/specify_cli/agents.py

@@ -9,6 +9,8 @@
 import hashlib
 import os
 import re
+import secrets
+import stat
 from copy import deepcopy
 from pathlib import Path
 from typing import Any, Dict, Iterable, List, Optional
@@ -1016,6 +1018,69 @@ def register_commands(
 
         return registered
 
+    @staticmethod
+    def _replace_file_text(dest: Path, content: str) -> None:
+        """Write ``content`` to ``dest`` by replacing its directory entry.
+
+        An in-place write reaches every hard link of the file, so an alias
+        linked to a file outside the project would carry the new text there
+        too. Writing a sibling temp file and renaming it over ``dest`` only
+        changes what ``dest`` names.
+
+        The replacement keeps an existing file's permission bits, and the
+        temp file is created with (at most) those bits and set to them before
+        any content is written, so the new text is never readable more widely
+        than the destination. A new file is created with mode 0666 so the
+        kernel applies the process umask, the same as an in-place write; the
+        umask itself is never changed.
+        The temp name has a fixed short length, so any name valid for
+        ``dest`` stays writable.
+        """
+        try:
+            dest_stat = os.lstat(dest)
+        except FileNotFoundError:
+            dest_stat = None
+        keep_mode = (
+            stat.S_IMODE(dest_stat.st_mode)
+            if dest_stat is not None and stat.S_ISREG(dest_stat.st_mode)
+            else None
+        )
+        # O_BINARY (Windows) leaves newline translation to the text wrapper
+        # below, as ``tempfile.mkstemp`` and ``Path.write_text`` do.
+        flags = (
+            os.O_WRONLY
+            | os.O_CREAT
+            | os.O_EXCL
+            | getattr(os, "O_NOFOLLOW", 0)
+            | getattr(os, "O_BINARY", 0)
+        )
+        for _attempt in range(100):
+            temp_path = dest.parent / f".speckit-{secrets.token_hex(8)}.tmp"
+            try:
+                fd = os.open(
+                    temp_path, flags, 0o666 if keep_mode is None else keep_mode
+                )
+            except FileExistsError:
+                continue
+            break
+        else:
+            raise FileExistsError(
+                f"Could not create a temporary file next to {dest}"
+            )
+        try:
+            # Wrap the descriptor first so a failing ``chmod`` cannot leak it:
+            # registration catches write errors and carries on.
+            with os.fdopen(fd, "w", encoding="utf-8") as fh:
+                if keep_mode is not None:
+                    # The umask may have cleared some of the destination's
+                    # bits; restore them before writing. This never widens
+                    # the mode beyond the destination's own.
+                    os.chmod(temp_path, keep_mode)
+                fh.write(content)
+            os.replace(temp_path, dest)
+        finally:
+            temp_path.unlink(missing_ok=True)
+
     @staticmethod
     def _write_registered_output(
         dest_file: Path,
@@ -1038,7 +1103,7 @@ def _write_registered_output(
         if not link_outputs or (agent_config or {}).get("dev_no_symlink"):
             if dest_file.is_symlink():
                 dest_file.unlink()
-            dest_file.write_text(content, encoding="utf-8")
+            CommandRegistrar._replace_file_text(dest_file, content)
             after_file_change(dest_file)
             return
 
@@ -1050,7 +1115,7 @@ def _write_registered_output(
         try:
             before_file_change(cache_file)
             cache_file.parent.mkdir(parents=True, exist_ok=True)
-            cache_file.write_text(content, encoding="utf-8")
+            CommandRegistrar._replace_file_text(cache_file, content)
             after_file_change(cache_file)
             if dest_file.exists() or dest_file.is_symlink():
                 dest_file.unlink()
@@ -1062,7 +1127,7 @@ def _write_registered_output(
             # functional by falling back to a copy.
             if dest_file.is_symlink():
                 dest_file.unlink()
-            dest_file.write_text(content, encoding="utf-8")
+            CommandRegistrar._replace_file_text(dest_file, content)
         after_file_change(dest_file)
 
     @staticmethod

src/specify_cli/presets/_manager.py

@@ -891,6 +891,10 @@ def remove(self, pack_id: str) -> bool:
                 registered_commands = commands_to_unregister
 
         # Unregister non-skill command files from AI agents.
+        if registered_commands:
+            registered_commands = self._drop_survivor_owned_aliases(
+                pack_id, registered_commands
+            )
         if registered_commands:
             self._unregister_commands(registered_commands)