Problem

APM deploys files into developer-curated directories (.github/prompts/, .github/skills/, .claude/agents/, etc.) — spaces developers actively manage by hand. The current integration system can destroy user-authored primitives in several ways:

1. HookIntegrator uses shutil.rmtree() on .github/hooks/scripts/ and .claude/hooks/ — unconditionally wiping all content including user scripts
2. SkillIntegrator (legacy path) deletes all skill directories not matching installed packages — destroying user-authored skills
3. Suffix naming pollution (-apm.prompt.md, -apm.agent.md) — users have complained about the naming convention
4. No collision detection — APM silently overwrites user files with the same name (instructions, skills)
5. apm prune removes packages from apm_modules/ but leaves stale integrated files in .github/ and .claude/

Solution: Unified deployed_files Manifest

Generalize the lockfile-based ownership tracking to ALL integrators. A single deployed_files field in apm.lock records every file path APM deployed:

dependencies:
  microsoft/code-review:
    version: "1.0.0"
    resolved: "https://github.com/microsoft/code-review"
    deployed_files:
      - .github/prompts/security-audit.prompt.md
      - .github/agents/reviewer.agent.md
      - .github/skills/code-review/
      - .github/hooks/pre-commit.json
      - .github/hooks/scripts/code-review/lint.sh
      - .claude/agents/reviewer.md
      - .claude/commands/security-audit.md

Behavior Changes

Install:

• Deploy with clean filenames (no -apm suffix)
• Skip + warn if file exists and is not in any package's deployed_files (user-authored)
• --force flag to overwrite user files explicitly
• Record all deployed paths in deployed_files

Uninstall:

• Remove only files listed in the uninstalled package's deployed_files
• No globs, no rmtree of entire directories, no guessing

Prune:

• After removing orphaned packages from apm_modules/, also remove their deployed_files from .github/ and .claude/

Migration

• Old -apm files are removed by existing sync logic on first install
• New clean-named files deployed and tracked in deployed_files
• Old lockfiles without deployed_files treated as "nothing managed" (safe default)

Scope

• deployed_files field in LockedDependency (replaces deployed_skills)
• All 6 integrators: record deployed paths, manifest-based cleanup
• Remove -apm suffix — deploy with clean filenames
• Collision detection: skip + warn, --force to override
• Fix HookIntegrator destructive rmtree calls
• Fix SkillIntegrator legacy fallback
• Prune cleans stale integrated files
• Backwards compatibility with old lockfiles

Blocks #112 (InstructionIntegrator PR #162 will rebase on this)