docs: clarify apm_modules is derived

[Aryan Singh K. (aryansk)]

Closes #2064

Summary

• document that apm_modules/ is derived and can be safely gitignored
• distinguish the committed lockfile/source manifest from regenerable installed content
• document the reinstall pattern for CI without inventing a currently unsupported persistence flag

Validation

• documentation-only change; patch syntax was checked against current main

[Copilot]

Pull request overview

Note

Copilot was unable to run its full agentic suite in this review.

Adds documentation clarifying that apm_modules/ is a derived, recreatable install directory and should typically be ignored in version control, positioning the lockfile as the durable source of truth.

Changes:

• Documented that apm_modules/ is derived from apm.yml + apm.lock.yaml and can be regenerated via apm install
• Added a recommended .gitignore entry for apm_modules/
• Noted CI/ephemeral workflow guidance and current lack of an automatic post-install cleanup flag

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