Refactor: Restructure pkgmgr into actions/, core/, and cli/ (full module breakup)

This commit introduces a large-scale structural refactor of the pkgmgr
codebase. All functionality has been moved from the previous flat
top-level layout into three clearly separated namespaces:

  • pkgmgr.actions      – high-level operations invoked by the CLI
  • pkgmgr.core         – pure logic, helpers, repository utilities,
                          versioning, git helpers, config IO, and
                          command resolution
  • pkgmgr.cli          – parser, dispatch, context, and command
                          handlers

Key improvements:
  - Moved all “branch”, “release”, “changelog”, repo-management
    actions, installer pipelines, and proxy execution logic into
    pkgmgr.actions.<domain>.
  - Reworked installer structure under
        pkgmgr.actions.repository.install.installers
    including OS-package installers, Nix, Python, and Makefile.
  - Consolidated all low-level functionality under pkgmgr.core:
        • git helpers → core/git
        • config load/save → core/config
        • repository helpers → core/repository
        • versioning & semver → core/version
        • command helpers (alias, resolve, run, ink) → core/command
  - Replaced pkgmgr.cli_core with pkgmgr.cli and updated all imports.
  - Added minimal __init__.py files for clean package exposure.
  - Updated all E2E, integration, and unit tests with new module paths.
  - Fixed patch targets so mocks point to the new structure.
  - Ensured backward compatibility at the CLI boundary (pkgmgr entry point unchanged).

This refactor produces a cleaner, layered architecture:
  - `core` = logic
  - `actions` = orchestrated behaviour
  - `cli` = user interface

Reference: ChatGPT-assisted refactor discussion
https://chatgpt.com/share/6938221c-e24c-800f-8317-7732cedf39b9

pkgmgr/actions/repository/status.py

@@ -0,0 +1,44 @@
+import sys
+import shutil
+
+from pkgmgr.actions.proxy import exec_proxy_command
+from pkgmgr.core.command.run import run_command
+from pkgmgr.core.repository.identifier import get_repo_identifier
+
+
+def status_repos(
+    selected_repos,
+    repositories_base_dir,
+    all_repos,
+    extra_args,
+    list_only: bool = False,
+    system_status: bool = False,
+    preview: bool = False,
+):
+    if system_status:
+        print("System status:")
+
+        # Arch / AUR updates (if yay / aur_builder is configured)
+        run_command("sudo -u aur_builder yay -Qu --noconfirm", preview=preview)
+
+        # Nix profile status (if Nix is available)
+        if shutil.which("nix") is not None:
+            print("\nNix profile status:")
+            try:
+                run_command("nix profile list", preview=preview)
+            except SystemExit as e:
+                print(f"[Warning] Failed to query Nix profiles: {e}")
+
+    if list_only:
+        for repo in selected_repos:
+            print(get_repo_identifier(repo, all_repos))
+    else:
+        exec_proxy_command(
+            "git",
+            selected_repos,
+            repositories_base_dir,
+            all_repos,
+            "status",
+            extra_args,
+            preview,
+        )