fix(cli): update standalone GitHub skills

[christso]

Summary

• route standalone GitHub tree-path skills through the skill-aware update preflight and reconciliation flow
• display the standalone skill name (setup-matt-pocock-skills) instead of its full source URL
• prevent retained or failed standalone checkouts from being advanced indirectly by generic sync
• account for disabled direct installs that share the same physical cache

Red reproduction

Built the CLI, installed the exact source in a disposable workspace, and selected Plugins → Update all:

- https://github.com/mattpocock/skills/tree/main/skills/engineering/setup-matt-pocock-skills (skipped)

Updated: 0  Skipped: 1  Failed: 0

Green E2E

bun run build
mkdir -p /tmp/allagents-skills-green/home /tmp/allagents-skills-green/workspace

# Run from /tmp/allagents-skills-green/workspace
env \
  ALLAGENTS_TEST_HOME=/tmp/allagents-skills-green/home \
  HOME=/tmp/allagents-skills-green/home \
  XDG_CONFIG_HOME=/tmp/allagents-skills-green/home/.config \
  XDG_CACHE_HOME=/tmp/allagents-skills-green/home/.cache \
  NO_COLOR=1 \
  /path/to/allagents/dist/index.js skill add \
  https://github.com/mattpocock/skills/tree/main/skills/engineering/setup-matt-pocock-skills \
  --scope project

# Make the disposable checkout genuinely stale while retaining the target skill.
cd /tmp/allagents-skills-green/home/.allagents/plugins/marketplaces/mattpocock-skills@main
git fetch --unshallow origin main
git reset --hard 321658273cb1d20b76026717d027d505790106d4

# Return to the disposable workspace, launch dist/index.js, then select:
# Plugins → Update all

Observed:

✓ setup-matt-pocock-skills (updated)

Updated: 1  Skipped: 0  Failed: 0

The cache advanced to origin/main, and the materialized skill matched the updated cached SKILL.md.

Automated verification

bun test tests/unit/cli/tui-plugin-update.test.ts
# 3 pass, 0 fail

bun run typecheck
bun run build

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