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/update.py

@@ -0,0 +1,68 @@
+import sys
+import shutil
+
+from pkgmgr.actions.repository.pull import pull_with_verification
+from pkgmgr.actions.repository.install import install_repos
+
+
+def update_repos(
+    selected_repos,
+    repositories_base_dir,
+    bin_dir,
+    all_repos,
+    no_verification,
+    system_update,
+    preview: bool,
+    quiet: bool,
+    update_dependencies: bool,
+    clone_mode: str,
+):
+    """
+    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,
+        repositories_base_dir,
+        all_repos,
+        [],
+        no_verification,
+        preview,
+    )
+
+    install_repos(
+        selected_repos,
+        repositories_base_dir,
+        bin_dir,
+        all_repos,
+        no_verification,
+        preview,
+        quiet,
+        clone_mode,
+        update_dependencies,
+    )
+
+    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)