docs: fix CLI reference drift from consistency reports #140 and #152

[Copilot]

Brings docs/cli-reference.md fully in sync with the current CLI surface, addressing all inconsistencies flagged by the automated CLI Consistency Checker in #140 and #152, plus reviewer feedback on the initial doc fix PR.

Changes

• Removed phantom --verbose flag from apm uninstall
• Added apm prune section
• Added ### apm mcp parent group section (apm mcp COMMAND [OPTIONS]); demoted list/search/show to #### — consistent with apm deps, apm runtime, apm config group patterns
• Added missing apm compile flags: --single-agents, -v/--verbose, --local-only, --clean
• Fixed apm compile --target choices to show [vscode|agents|claude|all]
• Added copilot runtime to supported runtimes list
• Fixed apm runtime setup argument description (was "remove", should be "install"); added --version TEXT option
• Added --yes to apm runtime remove
• Removed duplicate apm runtime status section
• Fixed runtime preference order: copilot → codex → llm (was codex → llm)
• Fixed apm search/apm show → apm mcp search/apm mcp show in Quick Start and Tips sections
• Removed internal dev note from apm deps update

Type of change

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

Testing

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

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