Is your feature request related to a problem? Please describe.

After the cli.py and apm_package.py refactoring in PR #224, several newly extracted modules exceed code quality thresholds (400-line file limit, 30-statement function limit). This makes the codebase harder to navigate, test, and maintain. Key pain points:

• 5 god files exceed the 400-line limit: install.py (1449), dependency.py (1024), deps.py (879), compile.py (739), uninstall.py (559)
• 9 god functions exceed 30 statements, with _install_apm_dependencies() (~250 stmts), uninstall() (~540 stmts), and DependencyReference.parse() (~380 stmts) being the worst
• ~85-line integration loop duplicated in full for cached vs. fresh packages in install.py
• 30+ overly broad exception handlers (except Exception:) across all modules, some swallowing errors silently
• String-typed dispatch (--only "apm"|"mcp") and boolean flag pairs where enums would be safer

Describe the solution you'd like

A phased refactoring (each phase is independently shippable) to bring all modules under quality thresholds:

Describe alternatives you've considered

• Do nothing: Acceptable short-term since PR Refactor cli.py and apm_package.py into focused modules (#172) #224 already reduced cli.py from 4500→80 lines, but the extracted modules inherited the same structural issues.
• Full rewrite: Over-engineered for current needs. Phased approach lets us ship incrementally and validate each change.

Additional context

• Full analysis was performed against the feat/172-refactor-cli-and-apm-package-modules branch (PR Refactor cli.py and apm_package.py into focused modules (#172) #224).
• Files analyzed (with line counts): install.py (1449), dependency.py (1024), deps.py (879), compile.py (739), uninstall.py (559), _helpers.py (405), validation.py (388), mcp.py (373), run.py (218), init.py (192), runtime.py (188), config.py (169), prune.py (143), update.py (136), list_cmd.py (102).
• Refactoring triggers checked: duplicated logic, god functions, primitive obsession, deep nesting, magic numbers/strings, dead code, broad exception handlers, god files, long parameter lists, boolean flag forking, string-typed dispatch, mixed abstraction levels.
• All phases must maintain 100% backward compatibility and pass uv run pytest tests/ -q --tb=short -x.