feat: apply manifest namespace to local .apm skills

[shreejaykurhade]

Description

This PR completes support for namespaced skill deployment by propagating the root apm.yml namespace into local .apm/skills integration.

The namespace behavior for skill deployment was already implemented; this change makes project-local skills follow the same rule as dependency-installed skills, so local sub-skills are deployed with names like acme.design.linting instead of unprefixed names.

This PR also adds regression coverage for the local .apm path and updates docs to reflect the expected namespaced skill folder behavior.

Fixes #739

Type of change

• [] Bug fix
• New feature
• Documentation
• Maintenance / refactor

Testing

• Tested locally
• All existing tests pass
• Added tests for new functionality (if applicable)

Issue-scoped tests passed locally:

• tests/unit/test_local_content_install.py
• tests/unit/integration/test_skill_integrator.py
• tests/integration/test_local_install.py -k "namespace or root_apm_skills_use_project_namespace"

Note:

• The full test suite currently reports 24 failed, 4453 passed, 160 skipped, 9 deselected, 11 warnings
• Those failures were not introduced as part of this issue-scoped change