docs: unify README doc domain, add deepagents-cli reference row, clarify presence markers

[dyoshikawa]

Summary

Resolves the actionable documentation follow-ups identified after PR #1710 (which restructured the "Supported Tools and Features" matrix into a presence overview), batched into one PR. Grouped by issue:

#1727 — Docs follow-ups from PR #1710

• Doc domain unified. README.md had a single "Supported Tools" link using the rulesync.dyoshikawa.com host while every other README doc link uses dyoshikawa.github.io/rulesync. The outlier is switched to the majority convention.
• deepagents-cli reference row added. The README presence overview lists deepagents-cli, but docs/reference/supported-tools.md (and its synced copy skills/rulesync/supported-tools.md) had no row. Added one with markers derived from the source-of-truth processors, not guessed:
  • rules ✅ — rules-processor.ts (supportsGlobal: false)
  • mcp ✅ 🌏 — mcp-processor.ts (supportsProject/supportsGlobal: true; no enabledTools/disabledTools → no 🔧)
  • subagents ✅, skills ✅ — native, project-only (no simulated/global)
  • hooks 🌏 — hooks-processor.ts (supportsProject: false, supportsGlobal: true → global-only)
  • commands / ignore / permissions blank — no deepagents entry
• The optional legend note (sub-item 3) is folded into the Review of PR #1710: Restructure supported tools matrix into presence overview #1724 mode-note below.

#1724 — Review of PR #1710 (presence overview)

• Presence-marker clarification. The README intro now states that a single ✅ means "supported in at least one mode (project, global, or simulated)", with Codex CLI commands (global-only) as a concrete example, and links to the full mode breakdown in the reference. This addresses the review's main concern that the flat ✅ hides global-only / simulated-only support.
  • Ground truth for the example: src/features/commands/codexcli-command.ts:18-21 throws unless { global: true }; docs/reference/supported-tools.md lists Codex CLI commands as 🌏 only.
• The format divergence between the README (presence-only) and the reference (multi-marker) is intentional and adequately bridged by the summary→detail link; no separate change is needed.

Not in scope (left open)

• Follow up Windsurf upstream updates: Cascade hooks, workflows, MCP, and rules #1701 (Windsurf upstream follow-up) — validation confirmed all the gaps are still real (Cascade hooks, workflows/commands, MCP, global rules, and the manual/model_decision trigger modes; none are implemented in rulesync today), but closing them is a large multi-feature buildout that needs maintainer scoping (priority/order, native-vs-simulated, project-vs-global coverage). It is intentionally not bundled into this docs PR and remains open.

Validation evidence

• Codebase (markers / ground truth): src/features/{rules,mcp,subagents,skills,hooks}/*-processor.ts deepagents meta; src/features/commands/codexcli-command.ts:18-21.
• README link inventory: 1 occurrence of rulesync.dyoshikawa.com vs 6 of dyoshikawa.github.io/rulesync before the fix.
• skills/rulesync/supported-tools.md is kept byte-identical to docs/reference/supported-tools.md by scripts/sync-skill-docs.ts.

Test plan

• pnpm cicheck — green: fmt:check / oxlint / eslint / typecheck pass; 5844 tests pass; check:sync-skill-docs, cspell (0 issues), and secretlint pass.

Closes #1727
Closes #1724

🤖 Generated with Claude Code

[dyoshikawa]

@dyoshikawa Thank you!