fix(skills): canonicalize standalone skill sources

[christso]

Closes #407

Summary

• canonicalize repeated standalone GitHub skill adds to the smallest shared repo container
• preserve a single plugin entry and merge the allowlist for same-repo skill URLs
• keep promoted container paths coherent for skill discovery and sync, including nested skill trees

E2E

bun run build

# Red E2E
TMPDIR=$(mktemp -d /tmp/allagents-407-red-XXXXXX)
mkdir -p "$TMPDIR/.allagents"
cat > "$TMPDIR/.allagents/workspace.yaml" <<'YAML'\nplugins:\n  - source: https://github.com/NousResearch/hermes-agent/tree/main/skills/research/llm-wiki\n    skills:\n      - llm-wiki\nclients:\n  - claude\nrepositories: []\nversion: 2\nYAML\n(cd "$TMPDIR" && node dist/index.js skill add https://github.com/NousResearch/hermes-agent/tree/main/skills/research/blogwatcher)\n\n# Green E2E\nTMPDIR=$(mktemp -d /tmp/allagents-407-green-XXXXXX)\nmkdir -p "$TMPDIR/.allagents"\ncat > "$TMPDIR/.allagents/workspace.yaml" <<'YAML'\nplugins:\n  - source: https://github.com/NousResearch/hermes-agent/tree/main/skills/research/llm-wiki\n    skills:\n      - llm-wiki\nclients:\n  - claude\nrepositories: []\nversion: 2\nYAML\n(cd "$TMPDIR" && \\\n  node /home/entity/projects/EntityProcess/allagents.worktrees/fix-407-source-canonicalization/dist/index.js skill add https://github.com/NousResearch/hermes-agent/tree/main/skills/research/blogwatcher && \\\n  node /home/entity/projects/EntityProcess/allagents.worktrees/fix-407-source-canonicalization/dist/index.js skill add https://github.com/NousResearch/hermes-agent/tree/main/skills/productivity/nano-pdf)\n```\n\nVerified the final workspace source is promoted to `https://github.com/NousResearch/hermes-agent/tree/main/skills` with a single plugin entry and the expected synced skills.

[cloudflare-workers-and-pages]

Deploying allagents with    Cloudflare Pages

Latest commit:	bb9decd
Status:	⚡️  Build in progress...

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