**Replace main.py with module-based entry point and unify CLI execution**

* Remove legacy *main.py* and introduce *pkgmgr* module entry via *python -m pkgmgr*
* Add ***main**.py* as the canonical entry point delegating to the CLI
* Export *PYTHONPATH=src* in Makefile to ensure reliable imports in dev and CI
* Update setup scripts (venv & nix) to use module execution
* Refactor all E2E tests to execute the real module entry instead of file paths

This aligns pkgmgr with standard Python packaging practices and simplifies testing, setup, and execution across environments.

https://chatgpt.com/share/693c9056-716c-800f-b583-fc9245eab2b4

scripts/setup/nix.sh

@@ -1,9 +1,9 @@
 # ------------------------------------------------------------
-# Nix shell mode: do not touch venv, only run main.py install
+# Nix shell mode: do not touch venv, only run install
 # ------------------------------------------------------------
 
 echo "[setup] Nix mode enabled (NIX_ENABLED=1)."
 echo "[setup] Skipping virtualenv creation and dependency installation."
-echo "[setup] Running main.py install via system python3..."
-python3 main.py install
+echo "[setup] Running install via system python3..."
+python3 -m pkgmgr install
 echo "[setup] Setup finished (Nix mode)."

scripts/setup/venv.sh

@@ -15,9 +15,6 @@ RC_LINE='if [ -d "${HOME}/.venvs/pkgmgr" ]; then . "${HOME}/.venvs/pkgmgr/bin/ac
 
 echo "[setup] Running in normal user mode (developer setup)."
 
-echo "[setup] Ensuring main.py is executable..."
-chmod +x main.py || true
-
 echo "[setup] Ensuring global virtualenv root: ${HOME}/.venvs"
 mkdir -p "${HOME}/.venvs"
 
@@ -90,8 +87,8 @@ for rc in "${HOME}/.bashrc" "${HOME}/.zshrc"; do
     fi
 done
 
-echo "[setup] Running main.py install via venv Python..."
-"${VENV_DIR}/bin/python" main.py install
+echo "[setup] Running install via venv Python..."
+"${VENV_DIR}/bin/python" -m pkgmgr install
 
 echo
 echo "[setup] Developer setup complete."