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

tests/e2e/test_integration_branch_commands.py

@@ -31,7 +31,7 @@ class TestIntegrationBranchCommands(unittest.TestCase):
         finally:
             sys.argv = original_argv
 
-    @patch("pkgmgr.cli_core.commands.branch.open_branch")
+    @patch("pkgmgr.cli.commands.branch.open_branch")
     def test_branch_open_with_name_and_base(self, mock_open_branch) -> None:
         """
         `pkgmgr branch open feature/test --base develop` must forward
@@ -47,7 +47,7 @@ class TestIntegrationBranchCommands(unittest.TestCase):
         self.assertEqual(kwargs.get("base_branch"), "develop")
         self.assertEqual(kwargs.get("cwd"), ".")
 
-    @patch("pkgmgr.cli_core.commands.branch.open_branch")
+    @patch("pkgmgr.cli.commands.branch.open_branch")
     def test_branch_open_without_name_uses_default_base(
         self,
         mock_open_branch,
@@ -68,7 +68,7 @@ class TestIntegrationBranchCommands(unittest.TestCase):
     # close subcommand
     # ------------------------------------------------------------------
 
-    @patch("pkgmgr.cli_core.commands.branch.close_branch")
+    @patch("pkgmgr.cli.commands.branch.close_branch")
     def test_branch_close_with_name_and_base(self, mock_close_branch) -> None:
         """
         `pkgmgr branch close feature/test --base develop` must forward
@@ -84,7 +84,7 @@ class TestIntegrationBranchCommands(unittest.TestCase):
         self.assertEqual(kwargs.get("base_branch"), "develop")
         self.assertEqual(kwargs.get("cwd"), ".")
 
-    @patch("pkgmgr.cli_core.commands.branch.close_branch")
+    @patch("pkgmgr.cli.commands.branch.close_branch")
     def test_branch_close_without_name_uses_default_base(
         self,
         mock_close_branch,

tests/e2e/test_integration_release_commands.py

@@ -6,7 +6,7 @@ End-to-end style integration tests for the `pkgmgr release` CLI command.
 
 These tests exercise the real top-level entry point (main.py) and mock
 the high-level helper used by the CLI wiring
-(pkgmgr.cli_core.commands.release.run_release) to ensure that argument
+(pkgmgr.cli.commands.release.run_release) to ensure that argument
 parsing and dispatch behave as expected, in particular the new `close`
 flag.
 
@@ -52,8 +52,8 @@ class TestIntegrationReleaseCommand(unittest.TestCase):
     # Behaviour without --close
     # ------------------------------------------------------------------
 
-    @patch("pkgmgr.cli_core.commands.release.run_release")
-    @patch("pkgmgr.cli_core.dispatch._select_repo_for_current_directory")
+    @patch("pkgmgr.cli.commands.release.run_release")
+    @patch("pkgmgr.cli.dispatch._select_repo_for_current_directory")
     def test_release_without_close_flag(
         self,
         mock_select_repo,
@@ -95,8 +95,8 @@ class TestIntegrationReleaseCommand(unittest.TestCase):
     # Behaviour with --close
     # ------------------------------------------------------------------
 
-    @patch("pkgmgr.cli_core.commands.release.run_release")
-    @patch("pkgmgr.cli_core.dispatch._select_repo_for_current_directory")
+    @patch("pkgmgr.cli.commands.release.run_release")
+    @patch("pkgmgr.cli.dispatch._select_repo_for_current_directory")
     def test_release_with_close_flag(
         self,
         mock_select_repo,

tests/e2e/test_integration_version_commands.py

@@ -28,7 +28,7 @@ import sys
 import unittest
 from typing import List
 
-from pkgmgr.load_config import load_config
+from pkgmgr.core.config.load import load_config
 
 # Resolve project root (the repo where main.py lives, e.g. /src)
 PROJECT_ROOT = os.path.abspath(