Enhance Nix flake installer to remove old profile entries before installation and update unit tests accordingly.

Includes:
- Added best-effort removal of existing 'package-manager' Nix profile entry.
- Updated install logic to avoid file conflicts.
- Extended unit tests to verify removal behavior and SystemExit-safe handling.

Conversation reference: https://chatgpt.com/share/69332bc4-a128-800f-a69c-fdc24c4cc7fe

pkgmgr/installers/nix_flake.py

@@ -6,6 +6,12 @@ Installer for Nix flakes.
 
 If a repository contains flake.nix and the 'nix' command is available, this
 installer will try to install profile outputs from the flake.
+
+Behavior:
+  - If flake.nix is present and `nix` exists on PATH:
+      * First remove any existing `package-manager` profile entry (best-effort).
+      * Then install the flake outputs (pkgmgr, default) via `nix profile install`.
+  - Any failure in `nix profile install` is treated as fatal (SystemExit).
 """
 
 import os
@@ -20,6 +26,7 @@ class NixFlakeInstaller(BaseInstaller):
     """Install Nix flake profiles for repositories that define flake.nix."""
 
     FLAKE_FILE = "flake.nix"
+    PROFILE_NAME = "package-manager"
 
     def supports(self, ctx: RepoContext) -> bool:
         """
@@ -32,11 +39,39 @@ class NixFlakeInstaller(BaseInstaller):
         flake_path = os.path.join(ctx.repo_dir, self.FLAKE_FILE)
         return os.path.exists(flake_path)
 
+    def _ensure_old_profile_removed(self, ctx: RepoContext) -> None:
+        """
+        Best-effort removal of an existing profile entry.
+
+        This handles the "already provides the following file" conflict by
+        removing previous `package-manager` installations before we install
+        the new one.
+
+        Any error in `nix profile remove` is intentionally ignored, because
+        a missing profile entry is not a fatal condition.
+        """
+        if shutil.which("nix") is None:
+            return
+
+        # We do NOT use run_command here, because we explicitly want to ignore
+        # the failure of `nix profile remove` (e.g. entry not present).
+        # Using `|| true` makes this idempotent.
+        cmd = f"nix profile remove {self.PROFILE_NAME} || true"
+        # This will still respect preview mode inside run_command.
+        try:
+            run_command(cmd, cwd=ctx.repo_dir, preview=ctx.preview)
+        except SystemExit:
+            # Ignore any error here: if the profile entry does not exist,
+            # that's fine and not a fatal condition.
+            pass
+
     def run(self, ctx: RepoContext) -> None:
         """
         Install Nix flake profile outputs (pkgmgr, default).
 
         Any failure in `nix profile install` is treated as fatal (SystemExit).
+        The "already installed / file conflict" situation is avoided by
+        removing the existing profile entry beforehand.
         """
         flake_path = os.path.join(ctx.repo_dir, self.FLAKE_FILE)
         if not os.path.exists(flake_path):
@@ -46,7 +81,11 @@ class NixFlakeInstaller(BaseInstaller):
             print("Warning: flake.nix found but 'nix' command not available. Skipping flake setup.")
             return
 
-        print("Nix flake detected, attempting to install profile output...")
+        print("Nix flake detected, attempting to install profile outputs...")
+
+        # Handle the "already installed" case up-front:
+        self._ensure_old_profile_removed(ctx)
+
         for output in ("pkgmgr", "default"):
             cmd = f"nix profile install {ctx.repo_dir}#{output}"
             try: