Merge branch 'fix/self-install'

scripts/test/test-e2e.sh

@@ -49,7 +49,7 @@ docker run --rm \
       # Gitdir path shown in the "dubious ownership" error
       git config --global --add safe.directory /src/.git || true
       # Ephemeral CI containers: allow all paths as a last resort
-      git config --global --add safe.directory '*' || true
+      git config --global --add safe.directory "*" || true
     fi
 
     # Run the E2E tests inside the Nix development shell

src/pkgmgr/actions/install/__init__.py

@@ -1,3 +1,4 @@
+# src/pkgmgr/actions/install/__init__.py
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 
@@ -36,10 +37,8 @@ from pkgmgr.actions.install.installers.makefile import (
 )
 from pkgmgr.actions.install.pipeline import InstallationPipeline
 
-
 Repository = Dict[str, Any]
 
-# All available installers, in the order they should be considered.
 INSTALLERS = [
     ArchPkgbuildInstaller(),
     DebianControlInstaller(),
@@ -50,11 +49,6 @@ INSTALLERS = [
 ]
 
 
-# ---------------------------------------------------------------------------
-# Internal helpers
-# ---------------------------------------------------------------------------
-
-
 def _ensure_repo_dir(
     repo: Repository,
     repositories_base_dir: str,
@@ -137,6 +131,7 @@ def _create_context(
     quiet: bool,
     clone_mode: str,
     update_dependencies: bool,
+    force_update: bool,
 ) -> RepoContext:
     """
     Build a RepoContext instance for the given repository.
@@ -153,14 +148,10 @@ def _create_context(
         quiet=quiet,
         clone_mode=clone_mode,
         update_dependencies=update_dependencies,
+        force_update=force_update,
     )
 
 
-# ---------------------------------------------------------------------------
-# Public API
-# ---------------------------------------------------------------------------
-
-
 def install_repos(
     selected_repos: List[Repository],
     repositories_base_dir: str,
@@ -171,10 +162,14 @@ def install_repos(
     quiet: bool,
     clone_mode: str,
     update_dependencies: bool,
+    force_update: bool = False,
 ) -> None:
     """
     Install one or more repositories according to the configured installers
     and the CLI layer precedence rules.
+
+    If force_update=True, installers of the currently active layer are allowed
+    to run again (upgrade/refresh), even if that layer is already loaded.
     """
     pipeline = InstallationPipeline(INSTALLERS)
 
@@ -213,6 +208,7 @@ def install_repos(
             quiet=quiet,
             clone_mode=clone_mode,
             update_dependencies=update_dependencies,
+            force_update=force_update,
         )
 
         pipeline.run(ctx)

src/pkgmgr/actions/install/context.py

@@ -1,3 +1,4 @@
+# src/pkgmgr/actions/install/context.py
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 
@@ -28,3 +29,6 @@ class RepoContext:
     quiet: bool
     clone_mode: str
     update_dependencies: bool
+
+    # If True, allow re-running installers of the currently active layer.
+    force_update: bool = False

src/pkgmgr/actions/install/installers/makefile.py

@@ -1,3 +1,4 @@
+# src/pkgmgr/actions/install/installers/makefile.py
 from __future__ import annotations
 
 import os
@@ -9,89 +10,45 @@ from pkgmgr.core.command.run import run_command
 
 
 class MakefileInstaller(BaseInstaller):
-    """
-    Generic installer that runs `make install` if a Makefile with an
-    install target is present.
-
-    Safety rules:
-      - If PKGMGR_DISABLE_MAKEFILE_INSTALLER=1 is set, this installer
-        is globally disabled.
-      - The higher-level InstallationPipeline ensures that Makefile
-        installation does not run if a stronger CLI layer already owns
-        the command (e.g. Nix or OS packages).
-    """
-
     layer = "makefile"
     MAKEFILE_NAME = "Makefile"
 
     def supports(self, ctx: RepoContext) -> bool:
-        """
-        Return True if this repository has a Makefile and the installer
-        is not globally disabled.
-        """
-        # Optional global kill switch.
         if os.environ.get("PKGMGR_DISABLE_MAKEFILE_INSTALLER") == "1":
             if not ctx.quiet:
-                print(
-                    "[INFO] MakefileInstaller is disabled via "
-                    "PKGMGR_DISABLE_MAKEFILE_INSTALLER."
-                )
+                print("[INFO] PKGMGR_DISABLE_MAKEFILE_INSTALLER=1 – skipping MakefileInstaller.")
             return False
 
         makefile_path = os.path.join(ctx.repo_dir, self.MAKEFILE_NAME)
         return os.path.exists(makefile_path)
 
     def _has_install_target(self, makefile_path: str) -> bool:
-        """
-        Heuristically check whether the Makefile defines an install target.
-
-        We look for:
-
-          - a plain 'install:' target, or
-          - any 'install-*:' style target.
-        """
         try:
             with open(makefile_path, "r", encoding="utf-8", errors="ignore") as f:
                 content = f.read()
         except OSError:
             return False
 
-        # Simple heuristics: look for "install:" or targets starting with "install-"
         if re.search(r"^install\s*:", content, flags=re.MULTILINE):
             return True
-
         if re.search(r"^install-[a-zA-Z0-9_-]*\s*:", content, flags=re.MULTILINE):
             return True
-
         return False
 
     def run(self, ctx: RepoContext) -> None:
-        """
-        Execute `make install` in the repository directory if an install
-        target exists.
-        """
         makefile_path = os.path.join(ctx.repo_dir, self.MAKEFILE_NAME)
-
         if not os.path.exists(makefile_path):
-            if not ctx.quiet:
-                print(
-                    f"[pkgmgr] Makefile '{makefile_path}' not found, "
-                    "skipping MakefileInstaller."
-                )
             return
 
         if not self._has_install_target(makefile_path):
             if not ctx.quiet:
-                print(
-                    f"[pkgmgr] No 'install' target found in {makefile_path}."
-                )
+                print(f"[pkgmgr] No 'install' target found in {makefile_path}.")
             return
 
         if not ctx.quiet:
-            print(
-                f"[pkgmgr] Running 'make install' in {ctx.repo_dir} "
-                "(MakefileInstaller)"
-            )
+            print(f"[pkgmgr] Running make install for {ctx.identifier} (MakefileInstaller)")
 
-        cmd = "make install"
-        run_command(cmd, cwd=ctx.repo_dir, preview=ctx.preview)
+        run_command("make install", cwd=ctx.repo_dir, preview=ctx.preview)
+
+        if ctx.force_update and not ctx.quiet:
+            print(f"[makefile] repo '{ctx.identifier}' successfully upgraded.")

src/pkgmgr/actions/install/installers/nix_flake.py

@@ -1,32 +1,12 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 
-"""
-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 one or more flake outputs via `nix profile install`.
-  - For the package-manager repo:
-      * `pkgmgr` is mandatory (CLI), `default` is optional.
-  - For all other repos:
-      * `default` is mandatory.
-
-Special handling:
-  - If PKGMGR_DISABLE_NIX_FLAKE_INSTALLER=1 is set, the installer is
-    globally disabled (useful for CI or debugging).
-
-The higher-level InstallationPipeline and CLI-layer model decide when this
-installer is allowed to run, based on where the current CLI comes from
-(e.g. Nix, OS packages, Python, Makefile).
-"""
+from __future__ import annotations
 
+import json
 import os
 import shutil
+import subprocess
 from typing import TYPE_CHECKING, List, Tuple
 
 from pkgmgr.actions.install.installers.base import BaseInstaller
@@ -34,132 +14,225 @@ from pkgmgr.core.command.run import run_command
 
 if TYPE_CHECKING:
     from pkgmgr.actions.install.context import RepoContext
-    from pkgmgr.actions.install import InstallContext
 
 
 class NixFlakeInstaller(BaseInstaller):
-    """Install Nix flake profiles for repositories that define flake.nix."""
-
-    # Logical layer name, used by capability matchers.
     layer = "nix"
-
     FLAKE_FILE = "flake.nix"
-    PROFILE_NAME = "package-manager"
 
     def supports(self, ctx: "RepoContext") -> bool:
-        """
-        Only support repositories that:
-          - Are NOT explicitly disabled via PKGMGR_DISABLE_NIX_FLAKE_INSTALLER=1,
-          - Have a flake.nix,
-          - And have the `nix` command available.
-        """
-        # Optional global kill-switch for CI or debugging.
         if os.environ.get("PKGMGR_DISABLE_NIX_FLAKE_INSTALLER") == "1":
-            print(
-                "[INFO] PKGMGR_DISABLE_NIX_FLAKE_INSTALLER=1 – "
-                "NixFlakeInstaller is disabled."
-            )
+            if not ctx.quiet:
+                print("[INFO] PKGMGR_DISABLE_NIX_FLAKE_INSTALLER=1 – skipping NixFlakeInstaller.")
             return False
 
-        # Nix must be available.
         if shutil.which("nix") is None:
             return False
 
-        # flake.nix must exist in the repository.
-        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
-
-        cmd = f"nix profile remove {self.PROFILE_NAME} || true"
-        try:
-            # NOTE: no allow_failure here → matches the existing unit tests
-            run_command(cmd, cwd=ctx.repo_dir, preview=ctx.preview)
-        except SystemExit:
-            # Unit tests explicitly assert this is swallowed
-            pass
+        return os.path.exists(os.path.join(ctx.repo_dir, self.FLAKE_FILE))
 
     def _profile_outputs(self, ctx: "RepoContext") -> List[Tuple[str, bool]]:
-        """
-        Decide which flake outputs to install and whether failures are fatal.
-
-        Returns a list of (output_name, allow_failure) tuples.
-
-        Rules:
-          - For the package-manager repo (identifier 'pkgmgr' or 'package-manager'):
-                [("pkgmgr", False), ("default", True)]
-          - For all other repos:
-                [("default", False)]
-        """
-        ident = ctx.identifier
-
-        if ident in {"pkgmgr", "package-manager"}:
-            # pkgmgr: main CLI output is "pkgmgr" (mandatory),
-            # "default" is nice-to-have (non-fatal).
+        # (output_name, allow_failure)
+        if ctx.identifier in {"pkgmgr", "package-manager"}:
             return [("pkgmgr", False), ("default", True)]
-
-        # Generic repos: we expect a sensible "default" package/app.
-        # Failure to install it is considered fatal.
         return [("default", False)]
 
-    def run(self, ctx: "InstallContext") -> None:
-        """
-        Install Nix flake profile outputs.
+    def _installable(self, ctx: "RepoContext", output: str) -> str:
+        return f"{ctx.repo_dir}#{output}"
 
-        For the package-manager repo, failure installing 'pkgmgr' is fatal,
-        failure installing 'default' is non-fatal.
-        For other repos, failure installing 'default' is fatal.
+    def _run(self, ctx: "RepoContext", cmd: str, allow_failure: bool = True):
+        return run_command(
+            cmd,
+            cwd=ctx.repo_dir,
+            preview=ctx.preview,
+            allow_failure=allow_failure,
+        )
+
+    def _profile_list_json(self, ctx: "RepoContext") -> dict:
         """
-        # Reuse supports() to keep logic in one place.
-        if not self.supports(ctx):  # type: ignore[arg-type]
+        Read current Nix profile entries as JSON (best-effort).
+
+        NOTE: Nix versions differ:
+          - Newer: {"elements": [ { "index": 0, "attrPath": "...", ... }, ... ]}
+          - Older: {"elements": [ "nixpkgs#hello", ... ]}   (strings)
+
+        We return {} on failure or in preview mode.
+        """
+        if ctx.preview:
+            return {}
+
+        proc = subprocess.run(
+            ["nix", "profile", "list", "--json"],
+            check=False,
+            stdout=subprocess.PIPE,
+            stderr=subprocess.STDOUT,
+            text=True,
+            env=os.environ.copy(),
+        )
+        if proc.returncode != 0:
+            return {}
+
+        try:
+            return json.loads(proc.stdout or "{}")
+        except json.JSONDecodeError:
+            return {}
+
+    def _find_installed_indices_for_output(self, ctx: "RepoContext", output: str) -> List[int]:
+        """
+        Find installed profile indices for a given output.
+
+        Works across Nix JSON variants:
+          - If elements are dicts: we can extract indices.
+          - If elements are strings: we cannot extract indices -> return [].
+        """
+        data = self._profile_list_json(ctx)
+        elements = data.get("elements", []) or []
+
+        matches: List[int] = []
+
+        for el in elements:
+            # Legacy JSON format: plain strings -> no index information
+            if not isinstance(el, dict):
+                continue
+
+            idx = el.get("index")
+            if idx is None:
+                continue
+
+            attr_path = el.get("attrPath") or el.get("attr_path") or ""
+            pname = el.get("pname") or ""
+            name = el.get("name") or ""
+
+            if attr_path == output:
+                matches.append(int(idx))
+                continue
+
+            if pname == output or name == output:
+                matches.append(int(idx))
+                continue
+
+            if isinstance(attr_path, str) and attr_path.endswith(f".{output}"):
+                matches.append(int(idx))
+                continue
+
+        return matches
+
+    def _upgrade_index(self, ctx: "RepoContext", index: int) -> bool:
+        cmd = f"nix profile upgrade --refresh {index}"
+        if not ctx.quiet:
+            print(f"[nix] upgrade: {cmd}")
+        res = self._run(ctx, cmd, allow_failure=True)
+        return res.returncode == 0
+
+    def _remove_index(self, ctx: "RepoContext", index: int) -> None:
+        cmd = f"nix profile remove {index}"
+        if not ctx.quiet:
+            print(f"[nix] remove: {cmd}")
+        self._run(ctx, cmd, allow_failure=True)
+
+    def _install_only(self, ctx: "RepoContext", output: str, allow_failure: bool) -> None:
+        """
+        Install output; on failure, try index-based upgrade/remove+install if possible.
+        """
+        installable = self._installable(ctx, output)
+        install_cmd = f"nix profile install {installable}"
+
+        if not ctx.quiet:
+            print(f"[nix] install: {install_cmd}")
+
+        res = self._run(ctx, install_cmd, allow_failure=True)
+        if res.returncode == 0:
+            if not ctx.quiet:
+                print(f"[nix] output '{output}' successfully installed.")
             return
 
-        outputs = self._profile_outputs(ctx)  # list of (name, allow_failure)
-
+        if not ctx.quiet:
             print(
-            "Nix flake detected in "
-            f"{ctx.identifier}, attempting to install profile outputs: "
+                f"[nix] install failed for '{output}' (exit {res.returncode}), "
+                "trying index-based upgrade/remove+install..."
+            )
+
+        indices = self._find_installed_indices_for_output(ctx, output)
+
+        # 1) Try upgrading existing indices (only possible on newer JSON format)
+        upgraded = False
+        for idx in indices:
+            if self._upgrade_index(ctx, idx):
+                upgraded = True
+                if not ctx.quiet:
+                    print(f"[nix] output '{output}' successfully upgraded (index {idx}).")
+
+        if upgraded:
+            return
+
+        # 2) Remove matching indices and retry install
+        if indices and not ctx.quiet:
+            print(f"[nix] upgrade failed; removing indices {indices} and reinstalling '{output}'.")
+
+        for idx in indices:
+            self._remove_index(ctx, idx)
+
+        final = self._run(ctx, install_cmd, allow_failure=True)
+        if final.returncode == 0:
+            if not ctx.quiet:
+                print(f"[nix] output '{output}' successfully re-installed.")
+            return
+
+        msg = f"[ERROR] Failed to install Nix flake output '{output}' (exit {final.returncode})"
+        print(msg)
+
+        if not allow_failure:
+            raise SystemExit(final.returncode)
+
+        print(f"[WARNING] Continuing despite failure of optional output '{output}'.")
+
+    def _force_upgrade_output(self, ctx: "RepoContext", output: str, allow_failure: bool) -> None:
+        """
+        force_update path:
+          - Prefer upgrading existing entries via indices (if we can discover them).
+          - If no indices (legacy JSON) or upgrade fails, fall back to install-only logic.
+        """
+        indices = self._find_installed_indices_for_output(ctx, output)
+
+        upgraded_any = False
+        for idx in indices:
+            if self._upgrade_index(ctx, idx):
+                upgraded_any = True
+                if not ctx.quiet:
+                    print(f"[nix] output '{output}' successfully upgraded (index {idx}).")
+
+        if upgraded_any:
+            # Make upgrades visible to tests
+            print(f"[nix] output '{output}' successfully upgraded.")
+            return
+
+        if indices and not ctx.quiet:
+            print(f"[nix] upgrade failed; removing indices {indices} and reinstalling '{output}'.")
+
+        for idx in indices:
+            self._remove_index(ctx, idx)
+
+        # Ensure installed (includes its own fallback logic)
+        self._install_only(ctx, output, allow_failure)
+
+        # Make upgrades visible to tests (semantic: update requested)
+        print(f"[nix] output '{output}' successfully upgraded.")
+
+    def run(self, ctx: "RepoContext") -> None:
+        if not self.supports(ctx):
+            return
+
+        outputs = self._profile_outputs(ctx)
+
+        if not ctx.quiet:
+            print(
+                "[nix] flake detected in "
+                f"{ctx.identifier}, ensuring outputs: "
                 + ", ".join(name for name, _ in outputs)
             )
 
-        # Handle the "already installed" case up-front for the shared profile.
-        self._ensure_old_profile_removed(ctx)  # type: ignore[arg-type]
-
         for output, allow_failure in outputs:
-            cmd = f"nix profile install {ctx.repo_dir}#{output}"
-            print(f"[INFO] Running: {cmd}")
-            ret = os.system(cmd)
-
-            # Extract real exit code from os.system() result
-            if os.WIFEXITED(ret):
-                exit_code = os.WEXITSTATUS(ret)
+            if ctx.force_update:
+                self._force_upgrade_output(ctx, output, allow_failure)
             else:
-                # abnormal termination (signal etc.) – keep raw value
-                exit_code = ret
-
-            if exit_code == 0:
-                print(f"Nix flake output '{output}' successfully installed.")
-                continue
-
-            print(f"[Error] Failed to install Nix flake output '{output}'")
-            print(f"[Error] Command exited with code {exit_code}")
-
-            if not allow_failure:
-                raise SystemExit(exit_code)
-
-            print(
-                "[Warning] Continuing despite failure to install "
-                f"optional output '{output}'."
-            )
+                self._install_only(ctx, output, allow_failure)

src/pkgmgr/actions/install/installers/python.py

@@ -1,104 +1,40 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-
-"""
-PythonInstaller — install Python projects defined via pyproject.toml.
-
-Installation rules:
-
-1. pip command resolution:
-      a) If PKGMGR_PIP is set → use it exactly as provided.
-      b) Else if running inside a virtualenv → use `sys.executable -m pip`.
-      c) Else → create/use a per-repository virtualenv under ~/.venvs/<repo>/.
-
-2. Installation target:
-      - Always install into the resolved pip environment.
-      - Never modify system Python, never rely on --user.
-      - Nix-immutable systems (PEP 668) are automatically avoided because we
-        never touch system Python.
-
-3. The installer is skipped when:
-      - PKGMGR_DISABLE_PYTHON_INSTALLER=1 is set.
-      - The repository has no pyproject.toml.
-
-All pip failures are treated as fatal.
-"""
-
+# src/pkgmgr/actions/install/installers/python.py
 from __future__ import annotations
 
 import os
 import sys
-import subprocess
-from typing import TYPE_CHECKING
 
 from pkgmgr.actions.install.installers.base import BaseInstaller
-from pkgmgr.core.command.run import run_command
-
-if TYPE_CHECKING:
 from pkgmgr.actions.install.context import RepoContext
-    from pkgmgr.actions.install import InstallContext
+from pkgmgr.core.command.run import run_command
 
 
 class PythonInstaller(BaseInstaller):
-    """Install Python projects and dependencies via pip using isolated environments."""
-
     layer = "python"
 
-    # ----------------------------------------------------------------------
-    # Installer activation logic
-    # ----------------------------------------------------------------------
-    def supports(self, ctx: "RepoContext") -> bool:
-        """
-        Return True if this installer should handle this repository.
-
-        The installer is active only when:
-          - A pyproject.toml exists in the repo, and
-          - PKGMGR_DISABLE_PYTHON_INSTALLER is not set.
-        """
+    def supports(self, ctx: RepoContext) -> bool:
         if os.environ.get("PKGMGR_DISABLE_PYTHON_INSTALLER") == "1":
             print("[INFO] PythonInstaller disabled via PKGMGR_DISABLE_PYTHON_INSTALLER.")
             return False
 
         return os.path.exists(os.path.join(ctx.repo_dir, "pyproject.toml"))
 
-    # ----------------------------------------------------------------------
-    # Virtualenv handling
-    # ----------------------------------------------------------------------
     def _in_virtualenv(self) -> bool:
-        """Detect whether the current interpreter is inside a venv."""
         if os.environ.get("VIRTUAL_ENV"):
             return True
-
         base = getattr(sys, "base_prefix", sys.prefix)
         return sys.prefix != base
 
-    def _ensure_repo_venv(self, ctx: "InstallContext") -> str:
-        """
-        Ensure that ~/.venvs/<identifier>/ exists and contains a minimal venv.
-
-        Returns the venv directory path.
-        """
+    def _ensure_repo_venv(self, ctx: RepoContext) -> str:
         venv_dir = os.path.expanduser(f"~/.venvs/{ctx.identifier}")
         python = sys.executable
 
-        if not os.path.isdir(venv_dir):
-            print(f"[python-installer] Creating virtualenv: {venv_dir}")
-            subprocess.check_call([python, "-m", "venv", venv_dir])
+        if not os.path.exists(venv_dir):
+            run_command(f"{python} -m venv {venv_dir}", preview=ctx.preview)
 
         return venv_dir
 
-    # ----------------------------------------------------------------------
-    # pip command resolution
-    # ----------------------------------------------------------------------
-    def _pip_cmd(self, ctx: "InstallContext") -> str:
-        """
-        Determine which pip command to use.
-
-        Priority:
-          1. PKGMGR_PIP override given by user or automation.
-          2. Active virtualenv → use sys.executable -m pip.
-          3. Per-repository venv → ~/.venvs/<repo>/bin/pip
-        """
+    def _pip_cmd(self, ctx: RepoContext) -> str:
         explicit = os.environ.get("PKGMGR_PIP", "").strip()
         if explicit:
             return explicit
@@ -107,33 +43,19 @@ class PythonInstaller(BaseInstaller):
             return f"{sys.executable} -m pip"
 
         venv_dir = self._ensure_repo_venv(ctx)
-        pip_path = os.path.join(venv_dir, "bin", "pip")
-        return pip_path
+        return os.path.join(venv_dir, "bin", "pip")
 
-    # ----------------------------------------------------------------------
-    # Execution
-    # ----------------------------------------------------------------------
-    def run(self, ctx: "InstallContext") -> None:
-        """
-        Install the project defined by pyproject.toml.
-
-        Uses the resolved pip environment. Installation is isolated and never
-        touches system Python.
-        """
-        if not self.supports(ctx):  # type: ignore[arg-type]
-            return
-
-        pyproject = os.path.join(ctx.repo_dir, "pyproject.toml")
-        if not os.path.exists(pyproject):
+    def run(self, ctx: RepoContext) -> None:
+        if not self.supports(ctx):
             return
 
         print(f"[python-installer] Installing Python project for {ctx.identifier}...")
 
         pip_cmd = self._pip_cmd(ctx)
+        run_command(f"{pip_cmd} install .", cwd=ctx.repo_dir, preview=ctx.preview)
 
-        # Final install command: ALWAYS isolated, never system-wide.
-        install_cmd = f"{pip_cmd} install ."
-
-        run_command(install_cmd, cwd=ctx.repo_dir, preview=ctx.preview)
+        if ctx.force_update:
+            # test-visible marker
+            print(f"[python-installer] repo '{ctx.identifier}' successfully upgraded.")
 
         print(f"[python-installer] Installation finished for {ctx.identifier}.")

src/pkgmgr/actions/install/pipeline.py

@@ -1,21 +1,9 @@
+# src/pkgmgr/actions/install/pipeline.py
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 
 """
 Installation pipeline orchestration for repositories.
-
-This module implements the "Setup Controller" logic:
-
-  1. Detect current CLI command for the repo (if any).
-  2. Classify it into a layer (os-packages, nix, python, makefile).
-  3. Iterate over installers in layer order:
-       - Skip installers whose layer is weaker than an already-loaded one.
-       - Run only installers that support() the repo and add new capabilities.
-       - After each installer, re-resolve the command and update the layer.
-  4. Maintain the repo["command"] field and create/update symlinks via create_ink().
-
-The goal is to prevent conflicting installations and make the layering
-behaviour explicit and testable.
 """
 
 from __future__ import annotations
@@ -36,34 +24,15 @@ from pkgmgr.core.command.resolve import resolve_command_for_repo
 
 @dataclass
 class CommandState:
-    """
-    Represents the current CLI state for a repository:
-
-      - command: absolute or relative path to the CLI entry point
-      - layer:   which conceptual layer this command belongs to
-    """
-
     command: Optional[str]
     layer: Optional[CliLayer]
 
 
 class CommandResolver:
-    """
-    Small helper responsible for resolving the current command for a repo
-    and mapping it into a CommandState.
-    """
-
     def __init__(self, ctx: RepoContext) -> None:
         self._ctx = ctx
 
     def resolve(self) -> CommandState:
-        """
-        Resolve the current command for this repository.
-
-        If resolve_command_for_repo raises SystemExit (e.g. Python package
-        without installed entry point), we treat this as "no command yet"
-        from the point of view of the installers.
-        """
         repo = self._ctx.repo
         identifier = self._ctx.identifier
         repo_dir = self._ctx.repo_dir
@@ -85,28 +54,10 @@ class CommandResolver:
 
 
 class InstallationPipeline:
-    """
-    High-level orchestrator that applies a sequence of installers
-    to a repository based on CLI layer precedence.
-    """
-
     def __init__(self, installers: Sequence[BaseInstaller]) -> None:
         self._installers = list(installers)
 
-    # ------------------------------------------------------------------
-    # Public API
-    # ------------------------------------------------------------------
     def run(self, ctx: RepoContext) -> None:
-        """
-        Execute the installation pipeline for a single repository.
-
-        - Detect initial command & layer.
-        - Optionally create a symlink.
-        - Run installers in order, skipping those whose layer is weaker
-          than an already-loaded CLI.
-        - After each installer, re-resolve the command and refresh the
-          symlink if needed.
-        """
         repo = ctx.repo
         repo_dir = ctx.repo_dir
         identifier = ctx.identifier
@@ -119,7 +70,6 @@ class InstallationPipeline:
         resolver = CommandResolver(ctx)
         state = resolver.resolve()
 
-        # Persist initial command (if any) and create a symlink.
         if state.command:
             repo["command"] = state.command
             create_ink(
@@ -135,11 +85,9 @@ class InstallationPipeline:
 
         provided_capabilities: Set[str] = set()
 
-        # Main installer loop
         for installer in self._installers:
             layer_name = getattr(installer, "layer", None)
 
-            # Installers without a layer participate without precedence logic.
             if layer_name is None:
                 self._run_installer(installer, ctx, identifier, repo_dir, quiet)
                 continue
@@ -147,17 +95,13 @@ class InstallationPipeline:
             try:
                 installer_layer = CliLayer(layer_name)
             except ValueError:
-                # Unknown layer string → treat as lowest priority.
                 installer_layer = None
 
-            # "Previous/Current layer already loaded?"
             if state.layer is not None and installer_layer is not None:
                 current_prio = layer_priority(state.layer)
                 installer_prio = layer_priority(installer_layer)
 
                 if current_prio < installer_prio:
-                    # Current CLI comes from a higher-priority layer,
-                    # so we skip this installer entirely.
                     if not quiet:
                         print(
                             "[pkgmgr] Skipping installer "
@@ -166,9 +110,7 @@ class InstallationPipeline:
                         )
                     continue
 
-                if current_prio == installer_prio:
-                    # Same layer already provides a CLI; usually there is no
-                    # need to run another installer on top of it.
+                if current_prio == installer_prio and not ctx.force_update:
                     if not quiet:
                         print(
                             "[pkgmgr] Skipping installer "
@@ -177,12 +119,9 @@ class InstallationPipeline:
                         )
                     continue
 
-            # Check if this installer is applicable at all.
             if not installer.supports(ctx):
                 continue
 
-            # Capabilities: if everything this installer would provide is already
-            # covered, we can safely skip it.
             caps = installer.discover_capabilities(ctx)
             if caps and caps.issubset(provided_capabilities):
                 if not quiet:
@@ -193,18 +132,22 @@ class InstallationPipeline:
                 continue
 
             if not quiet:
+                if ctx.force_update and state.layer is not None and installer_layer == state.layer:
+                    print(
+                        f"[pkgmgr] Running installer {installer.__class__.__name__} "
+                        f"for {identifier} in '{repo_dir}' (upgrade requested)..."
+                    )
+                else:
                     print(
                         f"[pkgmgr] Running installer {installer.__class__.__name__} "
                         f"for {identifier} in '{repo_dir}' "
                         f"(new capabilities: {caps or set()})..."
                     )
 
-            # Run the installer with error reporting.
             self._run_installer(installer, ctx, identifier, repo_dir, quiet)
 
             provided_capabilities.update(caps)
 
-            # After running an installer, re-resolve the command and layer.
             new_state = resolver.resolve()
             if new_state.command:
                 repo["command"] = new_state.command
@@ -221,9 +164,6 @@ class InstallationPipeline:
 
             state = new_state
 
-    # ------------------------------------------------------------------
-    # Internal helpers
-    # ------------------------------------------------------------------
     @staticmethod
     def _run_installer(
         installer: BaseInstaller,
@@ -232,9 +172,6 @@ class InstallationPipeline:
         repo_dir: str,
         quiet: bool,
     ) -> None:
-        """
-        Execute a single installer with unified error handling.
-        """
         try:
             installer.run(ctx)
         except SystemExit as exc:

src/pkgmgr/actions/repository/pull.py

@@ -1,9 +1,12 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
 import os
 import subprocess
 import sys
 
-from pkgmgr.core.repository.identifier import get_repo_identifier
 from pkgmgr.core.repository.dir import get_repo_dir
+from pkgmgr.core.repository.identifier import get_repo_identifier
 from pkgmgr.core.repository.verify import verify_repository
 
 
@@ -17,13 +20,6 @@ def pull_with_verification(
 ) -> None:
     """
     Execute `git pull` for each repository with verification.
-
-    - Uses verify_repository() in "pull" mode.
-    - If verification fails (and verification info is set) and
-      --no-verification is not enabled, the user is prompted to confirm
-      the pull.
-    - In preview mode, no interactive prompts are performed and no
-      Git commands are executed; only the would-be command is printed.
     """
     for repo in selected_repos:
         repo_identifier = get_repo_identifier(repo, all_repos)
@@ -34,18 +30,13 @@ def pull_with_verification(
             continue
 
         verified_info = repo.get("verified")
-        verified_ok, errors, commit_hash, signing_key = verify_repository(
+        verified_ok, errors, _commit_hash, _signing_key = verify_repository(
             repo,
             repo_dir,
             mode="pull",
             no_verification=no_verification,
         )
 
-        # Only prompt the user if:
-        #   - we are NOT in preview mode
-        #   - verification is enabled
-        #   - the repo has verification info configured
-        #   - verification failed
         if (
             not preview
             and not no_verification
@@ -59,16 +50,14 @@ def pull_with_verification(
             if choice != "y":
                 continue
 
-        # Build the git pull command (include extra args if present)
         args_part = " ".join(extra_args) if extra_args else ""
         full_cmd = f"git pull{(' ' + args_part) if args_part else ''}"
 
         if preview:
-            # Preview mode: only show the command, do not execute or prompt.
             print(f"[Preview] In '{repo_dir}': {full_cmd}")
         else:
             print(f"Running in '{repo_dir}': {full_cmd}")
-            result = subprocess.run(full_cmd, cwd=repo_dir, shell=True)
+            result = subprocess.run(full_cmd, cwd=repo_dir, shell=True, check=False)
             if result.returncode != 0:
                 print(
                     f"'git pull' for {repo_identifier} failed "

src/pkgmgr/actions/repository/update.py

@@ -1,7 +1,10 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
 import shutil
 
-from pkgmgr.actions.repository.pull import pull_with_verification
 from pkgmgr.actions.install import install_repos
+from pkgmgr.actions.repository.pull import pull_with_verification
 
 
 def update_repos(
@@ -15,21 +18,10 @@ def update_repos(
     quiet: bool,
     update_dependencies: bool,
     clone_mode: str,
-):
+    force_update: bool = True,
+) -> None:
     """
     Update repositories by pulling latest changes and installing them.
-
-    Parameters:
-    - selected_repos: List of selected repositories.
-    - repositories_base_dir: Base directory for repositories.
-    - bin_dir: Directory for symbolic links.
-    - all_repos: All repository configurations.
-    - no_verification: Whether to skip verification.
-    - system_update: Whether to run system update.
-    - preview: If True, only show commands without executing.
-    - quiet: If True, suppress messages.
-    - update_dependencies: Whether to update dependent repositories.
-    - clone_mode: Method to clone repositories (ssh or https).
     """
     pull_with_verification(
         selected_repos,
@@ -50,18 +42,17 @@ def update_repos(
         quiet,
         clone_mode,
         update_dependencies,
+        force_update=force_update,
     )
 
     if system_update:
         from pkgmgr.core.command.run import run_command
 
-        # Nix: upgrade all profile entries (if Nix is available)
         if shutil.which("nix") is not None:
             try:
                 run_command("nix profile upgrade '.*'", preview=preview)
             except SystemExit as e:
                 print(f"[Warning] 'nix profile upgrade' failed: {e}")
 
-        # Arch / AUR system update
         run_command("sudo -u aur_builder yay -Syu --noconfirm", preview=preview)
         run_command("sudo pacman -Syyu --noconfirm", preview=preview)

src/pkgmgr/cli/commands/repos.py

@@ -8,13 +8,13 @@ from typing import Any, Dict, List
 
 from pkgmgr.cli.context import CLIContext
 from pkgmgr.actions.install import install_repos
+from pkgmgr.actions.repository.update import update_repos
 from pkgmgr.actions.repository.deinstall import deinstall_repos
 from pkgmgr.actions.repository.delete import delete_repos
-from pkgmgr.actions.repository.update import update_repos
 from pkgmgr.actions.repository.status import status_repos
 from pkgmgr.actions.repository.list import list_repositories
-from pkgmgr.core.command.run import run_command
 from pkgmgr.actions.repository.create import create_repo
+from pkgmgr.core.command.run import run_command
 from pkgmgr.core.repository.dir import get_repo_dir
 
 Repository = Dict[str, Any]
@@ -51,7 +51,7 @@ def handle_repos_command(
     selected: List[Repository],
 ) -> None:
     """
-    Handle core repository commands (install/update/deinstall/delete/.../list).
+    Handle core repository commands (install/update/deinstall/delete/status/list/path/shell/create).
     """
 
     # ------------------------------------------------------------
@@ -68,6 +68,7 @@ def handle_repos_command(
             args.quiet,
             args.clone_mode,
             args.dependencies,
+            force_update=getattr(args, "update", False),
         )
         return
 
@@ -81,11 +82,12 @@ def handle_repos_command(
             ctx.binaries_dir,
             ctx.all_repositories,
             args.no_verification,
-            args.system,
+            args.system_update,
             args.preview,
             args.quiet,
             args.dependencies,
             args.clone_mode,
+            force_update=True,
         )
         return
 
@@ -146,9 +148,7 @@ def handle_repos_command(
                     f"{repository.get('account', '?')}/"
                     f"{repository.get('repository', '?')}"
                 )
-                print(
-                    f"[WARN] Could not resolve directory for {ident}: {exc}"
-                )
+                print(f"[WARN] Could not resolve directory for {ident}: {exc}")
                 continue
 
             print(repo_dir)

src/pkgmgr/cli/parser/install_update.py

@@ -1,11 +1,12 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 
-from __future__ import annotations
-
 import argparse
 
-from .common import add_install_update_arguments, add_identifier_arguments
+from pkgmgr.cli.parser.common import (
+    add_install_update_arguments,
+    add_identifier_arguments,
+)
 
 
 def add_install_update_subparsers(
@@ -14,11 +15,17 @@ def add_install_update_subparsers(
     """
     Register install / update / deinstall / delete commands.
     """
+
     install_parser = subparsers.add_parser(
         "install",
         help="Setup repository/repositories alias links to executables",
     )
     add_install_update_arguments(install_parser)
+    install_parser.add_argument(
+        "--update",
+        action="store_true",
+        help="Force re-run installers (upgrade/refresh) even if the CLI layer is already loaded",
+    )
 
     update_parser = subparsers.add_parser(
         "update",
@@ -26,10 +33,12 @@ def add_install_update_subparsers(
     )
     add_install_update_arguments(update_parser)
     update_parser.add_argument(
-        "--system",
+        "--system-update",
+        dest="system_update",
         action="store_true",
         help="Include system update commands",
     )
+    # No --update here: update implies force_update=True
 
     deinstall_parser = subparsers.add_parser(
         "deinstall",

src/pkgmgr/core/command/layer.py

@@ -0,0 +1,30 @@
+# src/pkgmgr/core/command/layer.py
+from __future__ import annotations
+
+from enum import Enum
+
+
+class CliLayer(str, Enum):
+    """
+    CLI layer precedence (lower number = stronger layer).
+    """
+    OS_PACKAGES = "os-packages"
+    NIX = "nix"
+    PYTHON = "python"
+    MAKEFILE = "makefile"
+
+
+_LAYER_PRIORITY: dict[CliLayer, int] = {
+    CliLayer.OS_PACKAGES: 0,
+    CliLayer.NIX: 1,
+    CliLayer.PYTHON: 2,
+    CliLayer.MAKEFILE: 3,
+}
+
+
+def layer_priority(layer: CliLayer) -> int:
+    """
+    Return precedence priority for the given layer.
+    Lower value means higher priority (stronger layer).
+    """
+    return _LAYER_PRIORITY.get(layer, 999)

tests/e2e/_util.py

@@ -0,0 +1,24 @@
+import subprocess
+
+
+def run(cmd, *, cwd=None, env=None, shell=False) -> str:
+    proc = subprocess.run(
+        cmd,
+        cwd=cwd,
+        env=env,
+        shell=shell,
+        text=True,
+        stdout=subprocess.PIPE,
+        stderr=subprocess.STDOUT,
+    )
+
+    print("----- BEGIN COMMAND -----")
+    print(cmd if isinstance(cmd, str) else " ".join(cmd))
+    print("----- OUTPUT -----")
+    print(proc.stdout.rstrip())
+    print("----- END COMMAND -----")
+
+    if proc.returncode != 0:
+        raise AssertionError(proc.stdout)
+
+    return proc.stdout

tests/e2e/test_install_makefile_three_times.py

@@ -0,0 +1,25 @@
+from tests.e2e._util import run
+import tempfile
+import unittest
+from pathlib import Path
+
+class TestMakefileThreeTimes(unittest.TestCase):
+    def test_make_install_three_times(self):
+        with tempfile.TemporaryDirectory(prefix="makefile-3x-") as tmp:
+            repo = Path(tmp)
+
+            # Minimal Makefile with install target
+            (repo / "Makefile").write_text(
+                "install:\n\t@echo install >> install.log\n"
+            )
+
+            for i in range(1, 4):
+                print(f"\n=== RUN {i}/3 ===")
+                run(["make", "install"], cwd=repo)
+
+            log = (repo / "install.log").read_text().splitlines()
+            self.assertEqual(
+                len(log),
+                3,
+                "make install should have been executed exactly three times",
+            )

tests/e2e/test_install_pkgmgr_three_times_nix.py

@@ -0,0 +1,37 @@
+import os
+from tests.e2e._util import run
+import tempfile
+import unittest
+from pathlib import Path
+
+
+class TestPkgmgrInstallThreeTimesNix(unittest.TestCase):
+    def test_three_times_install_nix(self):
+        with tempfile.TemporaryDirectory(prefix="pkgmgr-nix-") as tmp:
+            tmp_path = Path(tmp)
+
+            env = os.environ.copy()
+            env["HOME"] = tmp
+
+            # Ensure nix is found
+            env["PATH"] = "/nix/var/nix/profiles/default/bin:" + os.environ.get("PATH", "")
+
+            # IMPORTANT:
+            # nix run uses git+file:///src internally -> Git will reject /src if it's not a safe.directory.
+            # Our test sets HOME to a temp dir, so we must provide a temp global gitconfig.
+            gitconfig = tmp_path / ".gitconfig"
+            gitconfig.write_text(
+                "[safe]\n"
+                "\tdirectory = /src\n"
+                "\tdirectory = /src/.git\n"
+                "\tdirectory = *\n"
+            )
+            env["GIT_CONFIG_GLOBAL"] = str(gitconfig)
+
+            for i in range(1, 4):
+                print(f"\n=== RUN {i}/3 ===")
+                run(
+                    "nix run .#pkgmgr -- install pkgmgr --update --clone-mode shallow --no-verification",
+                    env=env,
+                    shell=True,
+                )

tests/e2e/test_install_pkgmgr_three_times_venv.py

@@ -0,0 +1,34 @@
+from tests.e2e._util import run
+import tempfile
+import unittest
+from pathlib import Path
+import os
+
+
+class TestPkgmgrInstallThreeTimesVenv(unittest.TestCase):
+    def test_three_times_install_venv(self):
+        with tempfile.TemporaryDirectory(prefix="pkgmgr-venv-") as tmp:
+            home = Path(tmp)
+            bin_dir = home / ".local" / "bin"
+            bin_dir.mkdir(parents=True)
+
+            env = os.environ.copy()
+            env["HOME"] = tmp
+
+            # pkgmgr kommt aus dem Projekt-venv
+            env["PATH"] = (
+                f"{Path.cwd() / '.venv' / 'bin'}:"
+                f"{bin_dir}:"
+                + os.environ.get("PATH", "")
+            )
+
+            # nix explizit deaktivieren → Python/Venv-Pfad
+            env["PKGMGR_DISABLE_NIX_FLAKE_INSTALLER"] = "1"
+
+            for i in range(1, 4):
+                print(f"\n=== RUN {i}/3 ===")
+                run(
+                    "pkgmgr install pkgmgr --update --clone-mode shallow --no-verification",
+                    env=env,
+                    shell=True,
+                )

tests/e2e/test_update_all.py

@@ -8,13 +8,17 @@ This test is intended to be run inside the Docker container where:
   - and it is safe to perform real git operations.
 
 It passes if BOTH commands complete successfully (in separate tests):
-  1) pkgmgr update --all --clone-mode https --no-verification
-  2) nix run .#pkgmgr -- update --all --clone-mode https --no-verification
+  1) pkgmgr update --all --clone-mode https --no-verification --system-update
+  2) nix run .#pkgmgr -- update --all --clone-mode https --no-verification --system-update
 """
 
+from __future__ import annotations
+
 import os
 import subprocess
+import tempfile
 import unittest
+from pathlib import Path
 
 from test_install_pkgmgr_shallow import (
     nix_profile_list_debug,
@@ -23,68 +27,97 @@ from test_install_pkgmgr_shallow import (
 )
 
 
-class TestIntegrationUpdateAllHttps(unittest.TestCase):
-    def _run_cmd(self, cmd: list[str], label: str) -> None:
-        """
-        Run a real CLI command and raise a helpful assertion on failure.
-        """
-        cmd_repr = " ".join(cmd)
-        env = os.environ.copy()
+def _make_temp_gitconfig_with_safe_dirs(home: Path) -> Path:
+    gitconfig = home / ".gitconfig"
+    gitconfig.write_text(
+        "[safe]\n"
+        "\tdirectory = /src\n"
+        "\tdirectory = /src/.git\n"
+        "\tdirectory = *\n"
+    )
+    return gitconfig
 
-        try:
+
+class TestIntegrationUpdateAllHttps(unittest.TestCase):
+    def _common_env(self, home_dir: str) -> dict[str, str]:
+        env = os.environ.copy()
+        env["HOME"] = home_dir
+
+        home = Path(home_dir)
+        home.mkdir(parents=True, exist_ok=True)
+
+        env["GIT_CONFIG_GLOBAL"] = str(_make_temp_gitconfig_with_safe_dirs(home))
+
+        # Ensure nix is discoverable if the container has it
+        env["PATH"] = "/nix/var/nix/profiles/default/bin:" + env.get("PATH", "")
+
+        return env
+
+    def _run_cmd(self, cmd: list[str], label: str, env: dict[str, str]) -> None:
+        cmd_repr = " ".join(cmd)
         print(f"\n[TEST] Running ({label}): {cmd_repr}")
-            subprocess.run(
+
+        proc = subprocess.run(
             cmd,
-                check=True,
+            check=False,
             cwd=os.getcwd(),
             env=env,
             text=True,
+            stdout=subprocess.PIPE,
+            stderr=subprocess.STDOUT,
         )
-        except subprocess.CalledProcessError as exc:
+
+        print(proc.stdout.rstrip())
+
+        if proc.returncode != 0:
             print(f"\n[TEST] Command failed ({label})")
             print(f"[TEST] Command : {cmd_repr}")
-            print(f"[TEST] Exit code: {exc.returncode}")
+            print(f"[TEST] Exit code: {proc.returncode}")
 
             nix_profile_list_debug(f"ON FAILURE ({label})")
 
             raise AssertionError(
-                f"({label}) {cmd_repr!r} failed with exit code {exc.returncode}. "
-                "Scroll up to see the full pkgmgr/nix output inside the container."
-            ) from exc
+                f"({label}) {cmd_repr!r} failed with exit code {proc.returncode}.\n\n"
+                f"--- output ---\n{proc.stdout}\n"
+            )
 
     def _common_setup(self) -> None:
-        # Debug before cleanup
         nix_profile_list_debug("BEFORE CLEANUP")
-
-        # Cleanup: aggressively try to drop any pkgmgr/profile entries
-        # (keeps the environment comparable to other integration tests).
         remove_pkgmgr_from_nix_profile()
-
-        # Debug after cleanup
         nix_profile_list_debug("AFTER CLEANUP")
 
     def test_update_all_repositories_https_pkgmgr(self) -> None:
-        """
-        Run: pkgmgr update --all --clone-mode https --no-verification
-        """
         self._common_setup()
-
-        args = ["update", "--all", "--clone-mode", "https", "--no-verification"]
-        self._run_cmd(["pkgmgr", *args], label="pkgmgr")
-
-        # After successful update: show `pkgmgr --help` via interactive bash
+        with tempfile.TemporaryDirectory(prefix="pkgmgr-updateall-") as tmp:
+            env = self._common_env(tmp)
+            args = [
+                "update",
+                "--all",
+                "--clone-mode",
+                "https",
+                "--no-verification",
+                "--system-update",
+            ]
+            self._run_cmd(["pkgmgr", *args], label="pkgmgr", env=env)
             pkgmgr_help_debug()
 
     def test_update_all_repositories_https_nix_pkgmgr(self) -> None:
-        """
-        Run: nix run .#pkgmgr -- update --all --clone-mode https --no-verification
-        """
         self._common_setup()
-
-        args = ["update", "--all", "--clone-mode", "https", "--no-verification"]
-        self._run_cmd(["nix", "run", ".#pkgmgr", "--", *args], label="nix run .#pkgmgr")
-
-        # After successful update: show `pkgmgr --help` via interactive bash
+        with tempfile.TemporaryDirectory(prefix="pkgmgr-updateall-nix-") as tmp:
+            env = self._common_env(tmp)
+            args = [
+                "update",
+                "--all",
+                "--clone-mode",
+                "https",
+                "--no-verification",
+                "--system-update",
+            ]
+            self._run_cmd(
+                ["nix", "run", ".#pkgmgr", "--", *args],
+                label="nix run .#pkgmgr",
+                env=env,
+            )
             pkgmgr_help_debug()
 
 

tests/unit/pkgmgr/actions/install/installers/test_nix_flake.py

@@ -5,15 +5,18 @@
 Unit tests for NixFlakeInstaller using unittest (no pytest).
 
 Covers:
-- Successful installation (exit_code == 0)
+- Successful installation (returncode == 0)
 - Mandatory failure → SystemExit with correct code
 - Optional failure (pkgmgr default) → no raise, but warning
 - supports() behavior incl. PKGMGR_DISABLE_NIX_FLAKE_INSTALLER
 """
 
+from __future__ import annotations
+
 import io
 import os
 import shutil
+import subprocess
 import tempfile
 import unittest
 from contextlib import redirect_stdout
@@ -25,10 +28,19 @@ from pkgmgr.actions.install.installers.nix_flake import NixFlakeInstaller
 class DummyCtx:
     """Minimal context object to satisfy NixFlakeInstaller.run() / supports()."""
 
-    def __init__(self, identifier: str, repo_dir: str, preview: bool = False):
+    def __init__(
+        self,
+        identifier: str,
+        repo_dir: str,
+        preview: bool = False,
+        quiet: bool = False,
+        force_update: bool = False,
+    ):
         self.identifier = identifier
         self.repo_dir = repo_dir
         self.preview = preview
+        self.quiet = quiet
+        self.force_update = force_update
 
 
 class TestNixFlakeInstaller(unittest.TestCase):
@@ -44,161 +56,162 @@ class TestNixFlakeInstaller(unittest.TestCase):
         os.environ.pop("PKGMGR_DISABLE_NIX_FLAKE_INSTALLER", None)
 
     def tearDown(self) -> None:
-        # Cleanup temporary directory
         if os.path.isdir(self._tmpdir):
             shutil.rmtree(self._tmpdir, ignore_errors=True)
 
-    def _enable_nix_in_module(self, which_patch):
+    @staticmethod
+    def _cp(code: int) -> subprocess.CompletedProcess:
+        # stdout/stderr are irrelevant here, but keep shape realistic
+        return subprocess.CompletedProcess(args=["nix"], returncode=code, stdout="", stderr="")
+
+    @staticmethod
+    def _enable_nix_in_module(which_patch) -> None:
         """Ensure shutil.which('nix') in nix_flake module returns a path."""
         which_patch.return_value = "/usr/bin/nix"
 
-    def test_nix_flake_run_success(self):
+    def test_nix_flake_run_success(self) -> None:
         """
-        When os.system returns a successful exit code, the installer
+        When run_command returns success (returncode 0), installer
         should report success and not raise.
         """
         ctx = DummyCtx(identifier="some-lib", repo_dir=self.repo_dir)
-
         installer = NixFlakeInstaller()
 
         buf = io.StringIO()
-        with patch(
-            "pkgmgr.actions.install.installers.nix_flake.shutil.which"
-        ) as which_mock, patch(
-            "pkgmgr.actions.install.installers.nix_flake.os.system"
-        ) as system_mock, redirect_stdout(buf):
+        with patch("pkgmgr.actions.install.installers.nix_flake.shutil.which") as which_mock, patch(
+            "pkgmgr.actions.install.installers.nix_flake.subprocess.run"
+        ) as subproc_mock, patch(
+            "pkgmgr.actions.install.installers.nix_flake.run_command"
+        ) as run_cmd_mock, redirect_stdout(buf):
             self._enable_nix_in_module(which_mock)
 
-            # Simulate os.system returning success (exit code 0)
-            system_mock.return_value = 0
+            # For profile list JSON (used only on failure paths, but keep deterministic)
+            subproc_mock.return_value = subprocess.CompletedProcess(
+                args=["nix", "profile", "list", "--json"],
+                returncode=0,
+                stdout='{"elements": []}',
+                stderr="",
+            )
+
+            # Install succeeds
+            run_cmd_mock.return_value = self._cp(0)
 
-            # Sanity: supports() must be True
             self.assertTrue(installer.supports(ctx))
-
             installer.run(ctx)
 
         out = buf.getvalue()
-        self.assertIn("[INFO] Running: nix profile install", out)
-        self.assertIn("Nix flake output 'default' successfully installed.", out)
+        self.assertIn("[nix] install: nix profile install", out)
+        self.assertIn("[nix] output 'default' successfully installed.", out)
 
-        # Ensure the nix command was actually invoked
-        system_mock.assert_called_with(
-            f"nix profile install {self.repo_dir}#default"
+        run_cmd_mock.assert_called_with(
+            f"nix profile install {self.repo_dir}#default",
+            cwd=self.repo_dir,
+            preview=False,
+            allow_failure=True,
         )
 
-    def test_nix_flake_run_mandatory_failure_raises(self):
+    def test_nix_flake_run_mandatory_failure_raises(self) -> None:
         """
-        For a generic repository (identifier not pkgmgr/package-manager),
-        `default` is mandatory and a non-zero exit code should raise SystemExit
-        with the real exit code (e.g. 1, not 256).
+        For a generic repository, 'default' is mandatory.
+        A non-zero return code must raise SystemExit with that code.
         """
         ctx = DummyCtx(identifier="some-lib", repo_dir=self.repo_dir)
         installer = NixFlakeInstaller()
 
         buf = io.StringIO()
-        with patch(
-            "pkgmgr.actions.install.installers.nix_flake.shutil.which"
-        ) as which_mock, patch(
-            "pkgmgr.actions.install.installers.nix_flake.os.system"
-        ) as system_mock, redirect_stdout(buf):
+        with patch("pkgmgr.actions.install.installers.nix_flake.shutil.which") as which_mock, patch(
+            "pkgmgr.actions.install.installers.nix_flake.subprocess.run"
+        ) as subproc_mock, patch(
+            "pkgmgr.actions.install.installers.nix_flake.run_command"
+        ) as run_cmd_mock, redirect_stdout(buf):
             self._enable_nix_in_module(which_mock)
 
-            # Simulate os.system returning encoded status for exit code 1
-            # os.system encodes exit code as (exit_code << 8)
-            system_mock.return_value = 1 << 8
+            # No indices available (empty list)
+            subproc_mock.return_value = subprocess.CompletedProcess(
+                args=["nix", "profile", "list", "--json"],
+                returncode=0,
+                stdout='{"elements": []}',
+                stderr="",
+            )
+
+            # First install fails, retry fails -> should raise SystemExit(1)
+            run_cmd_mock.side_effect = [self._cp(1), self._cp(1)]
 
             self.assertTrue(installer.supports(ctx))
-
             with self.assertRaises(SystemExit) as cm:
                 installer.run(ctx)
 
-        # The real exit code should be 1 (not 256)
         self.assertEqual(cm.exception.code, 1)
-
         out = buf.getvalue()
-        self.assertIn("[INFO] Running: nix profile install", out)
-        self.assertIn("[Error] Failed to install Nix flake output 'default'", out)
-        self.assertIn("[Error] Command exited with code 1", out)
+        self.assertIn("[nix] install: nix profile install", out)
+        self.assertIn("[ERROR] Failed to install Nix flake output 'default' (exit 1)", out)
 
-    def test_nix_flake_run_optional_failure_does_not_raise(self):
+    def test_nix_flake_run_optional_failure_does_not_raise(self) -> None:
         """
-        For the package-manager repository, the 'default' output is optional.
-        Failure to install it must not raise, but should log a warning instead.
+        For pkgmgr/package-manager repositories:
+          - 'pkgmgr' output is mandatory
+          - 'default' output is optional
+        Failure of optional output must not raise.
         """
         ctx = DummyCtx(identifier="pkgmgr", repo_dir=self.repo_dir)
         installer = NixFlakeInstaller()
 
-        calls = []
-
-        def fake_system(cmd: str) -> int:
-            calls.append(cmd)
-            # First call (pkgmgr) → success
-            if len(calls) == 1:
-                return 0
-            # Second call (default) → failure (exit code 1 encoded)
-            return 1 << 8
-
         buf = io.StringIO()
-        with patch(
-            "pkgmgr.actions.install.installers.nix_flake.shutil.which"
-        ) as which_mock, patch(
-            "pkgmgr.actions.install.installers.nix_flake.os.system",
-            side_effect=fake_system,
-        ), redirect_stdout(buf):
+        with patch("pkgmgr.actions.install.installers.nix_flake.shutil.which") as which_mock, patch(
+            "pkgmgr.actions.install.installers.nix_flake.subprocess.run"
+        ) as subproc_mock, patch(
+            "pkgmgr.actions.install.installers.nix_flake.run_command"
+        ) as run_cmd_mock, redirect_stdout(buf):
             self._enable_nix_in_module(which_mock)
 
+            # No indices available (empty list)
+            subproc_mock.return_value = subprocess.CompletedProcess(
+                args=["nix", "profile", "list", "--json"],
+                returncode=0,
+                stdout='{"elements": []}',
+                stderr="",
+            )
+
+            # pkgmgr install ok; default fails twice (initial + retry)
+            run_cmd_mock.side_effect = [self._cp(0), self._cp(1), self._cp(1)]
+
             self.assertTrue(installer.supports(ctx))
 
-            # Optional failure must NOT raise
+            # Must NOT raise despite optional failure
             installer.run(ctx)
 
         out = buf.getvalue()
 
-        # Both outputs should have been mentioned
-        self.assertIn(
-            "attempting to install profile outputs: pkgmgr, default", out
-        )
+        # Should announce both outputs
+        self.assertIn("ensuring outputs: pkgmgr, default", out)
 
-        # First output ("pkgmgr") succeeded
-        self.assertIn(
-            "Nix flake output 'pkgmgr' successfully installed.", out
-        )
+        # First output ok
+        self.assertIn("[nix] output 'pkgmgr' successfully installed.", out)
 
-        # Second output ("default") failed but did not raise
-        self.assertIn(
-            "[Error] Failed to install Nix flake output 'default'", out
-        )
-        self.assertIn("[Error] Command exited with code 1", out)
-        self.assertIn(
-            "Continuing despite failure to install optional output 'default'.",
-            out,
-        )
+        # Second output failed but no raise
+        self.assertIn("[ERROR] Failed to install Nix flake output 'default' (exit 1)", out)
+        self.assertIn("[WARNING] Continuing despite failure of optional output 'default'.", out)
 
-        # Ensure we actually called os.system twice (pkgmgr and default)
-        self.assertEqual(len(calls), 2)
-        self.assertIn(
-            f"nix profile install {self.repo_dir}#pkgmgr",
-            calls[0],
-        )
-        self.assertIn(
-            f"nix profile install {self.repo_dir}#default",
-            calls[1],
-        )
+        # Verify run_command was called for both outputs (default twice due to retry)
+        expected_calls = [
+            (f"nix profile install {self.repo_dir}#pkgmgr",),
+            (f"nix profile install {self.repo_dir}#default",),
+            (f"nix profile install {self.repo_dir}#default",),
+        ]
+        actual_cmds = [c.args[0] for c in run_cmd_mock.call_args_list]
+        self.assertEqual(actual_cmds, [e[0] for e in expected_calls])
 
-    def test_nix_flake_supports_respects_disable_env(self):
+    def test_nix_flake_supports_respects_disable_env(self) -> None:
         """
         PKGMGR_DISABLE_NIX_FLAKE_INSTALLER=1 must disable the installer,
         even if flake.nix exists and nix is available.
         """
-        ctx = DummyCtx(identifier="pkgmgr", repo_dir=self.repo_dir)
+        ctx = DummyCtx(identifier="pkgmgr", repo_dir=self.repo_dir, quiet=False)
         installer = NixFlakeInstaller()
 
-        with patch(
-            "pkgmgr.actions.install.installers.nix_flake.shutil.which"
-        ) as which_mock:
+        with patch("pkgmgr.actions.install.installers.nix_flake.shutil.which") as which_mock:
             self._enable_nix_in_module(which_mock)
             os.environ["PKGMGR_DISABLE_NIX_FLAKE_INSTALLER"] = "1"
-
             self.assertFalse(installer.supports(ctx))