feat(cli): support installing specific skills

[christso]

Summary

Closes #197

• Add --skill flag to plugin install for cherry-picking specific skills from a plugin
• Add enabledSkills (allowlist) config field to complement existing disabledSkills (denylist)
• Update plugin skills add/remove to detect allowlist vs denylist mode automatically
• Fix pre-existing bug where skill pruning on uninstall failed for marketplace-resolved plugin names
• Fix per-plugin scoping of enabledSkills filter (was incorrectly applied globally)
• Fix plugin name consistency between skills listing and sync pipeline
• Eliminate double sync on plugin install --skill

Usage

# Install plugin with only specific skills enabled
allagents plugin install superpowers@marketplace --skill brainstorming
allagents plugin install superpowers@marketplace --skill brainstorming --skill tdd

# After install, manage skills normally
allagents plugin skills add verification        # adds to enabledSkills
allagents plugin skills remove brainstorming     # removes from enabledSkills
allagents plugin skills list                     # shows enabled/disabled status

Config model

plugins:
  - superpowers@marketplace
enabledSkills:
  - superpowers:brainstorming
  - superpowers:test-driven-development

When enabledSkills has entries for a plugin, only those skills sync (allowlist). When absent, existing disabledSkills behavior applies (denylist). Uninstalling a plugin cleans up both lists.

Test plan

• Unit tests: 848 pass, 0 fail
• Lint and typecheck pass
• E2E: full workflow validated (see below)

E2E steps reproduced

bun run build
TESTDIR=$(mktemp -d /tmp/e2e-skills-XXXXXX)
mkdir -p "$TESTDIR/.allagents"
echo 'repositories: []\nplugins: []\nclients: [claude]' > "$TESTDIR/.allagents/workspace.yaml"
cd "$TESTDIR"

# Test 1: Install with --skill (only brainstorming synced, 1 skill dir)
./dist/index.js plugin install superpowers@obra/superpowers --skill brainstorming
# PASS: 1 skill synced, enabledSkills key = superpowers:brainstorming

# Test 2: skills list shows correct enabled/disabled status
./dist/index.js plugin skills list --scope project
# PASS: brainstorming enabled, all others disabled

# Test 3: skills add in allowlist mode
./dist/index.js plugin skills add test-driven-development --scope project
# PASS: test-driven-development synced

# Test 4: skills remove in allowlist mode
./dist/index.js plugin skills remove brainstorming --scope project
# PASS: brainstorming removed from sync

# Test 5: uninstall cleans up enabledSkills
./dist/index.js plugin uninstall superpowers --scope project
# PASS: enabledSkills removed from config

rm -rf "$TESTDIR"

All 6 E2E assertions passed.

[cloudflare-workers-and-pages]

Deploying allagents with    Cloudflare Pages

Latest commit:	6e74cfe
Status:	✅  Deploy successful!
Preview URL:	https://d340d538.allagents.pages.dev
Branch Preview URL:	https://feat-197-install-specific-sk.allagents.pages.dev

View logs