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

[danielmeppiel]

Description

Fixes all doc-vs-CLI inconsistencies found by the automated CLI Consistency Checker in #140 and #152.

Changes

Fix	Severity	Source
Remove phantom --verbose from apm uninstall	High (#140) / Medium (#152)	Both
Add apm prune section	High (#152)	#152 only
Add apm mcp list section	High (#152) / Medium (#140)	Both
Add 4 missing apm compile flags (--single-agents, -v/--verbose, --local-only, --clean)	Medium	Both
Fix apm compile --target to show [vscode|agents|claude|all]	Low/Medium	Both
Add copilot to supported runtimes	Medium	Both
Fix apm runtime setup argument description ("remove" → "install")	Medium	Both
Add --version TEXT to apm runtime setup	Medium	Both
Add --yes to apm runtime remove	Low (#140)	Both
Remove duplicate apm runtime status section	Medium (#152)	#152 only
Fix apm search/apm show → apm mcp search/apm mcp show in Quick Start	High (#140)	#140 only
Fix apm search → apm mcp search in Tips section	High (#140)	#140 only
Remove internal dev note from apm deps update	Medium/Low	Both

Type of change

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

Fixes #152
Supersedes #140

[Copilot]

Pull request overview

Updates the CLI reference documentation to resolve drift reported by the automated CLI Consistency Checker (issues #140 and #152), bringing docs/cli-reference.md back in sync with the current APM CLI surface.

Changes:

• Removes the nonexistent --verbose flag from apm uninstall docs and fixes apm mcp search/show references in the Quick Start + Tips sections.
• Adds missing documentation for apm prune, apm mcp list, and several apm compile flags/--target choices.
• Updates runtime docs to include the copilot runtime and corrects apm runtime setup/remove argument/options content (including de-duplicating runtime status).

Comments suppressed due to low confidence (2)

docs/cli-reference.md:506

• apm mcp list’s --limit option has a default of 20 in the CLI (@click.option("--limit", default=20, ...)), but the docs don’t mention the default (whereas apm mcp search does). To keep the CLI reference accurate, add “(default: 20)” to the --limit description.

**Options:**
- `--limit INTEGER` - Number of results to show

docs/cli-reference.md:899

• The copilot runtime description here doesn’t match the CLI/runtime manager description (“GitHub Copilot CLI with native MCP integration”). Aligning the wording will reduce confusion about what exactly gets installed/managed when users choose copilot.

**Supported Runtimes:**
- **`copilot`** - GitHub Copilot coding agent
- **`codex`** - OpenAI Codex CLI with GitHub Models support
- **`llm`** - Simon Willison's LLM library with multiple providers

[danielmeppiel]

@copilot address all the pull request review comments appropriately

[Copilot]

@danielmeppiel I've opened a new pull request, #161, to work on those changes. Once the pull request is ready, I'll request review from you.