feat: provider integration manifest with Codex pilot (closes #36)

[Minitour]

Summary

• Drop the skills package dependency and absorb its 39-entry agent registry into a new Provider Integration Manifest (src/shared/providers/). The manifest is the single source of truth for skill paths (replacing vercel-labs/skills), MCP configuration, instructions files, rules directories, subagent formats, and plugin manifest paths.
• Purely declarative provider registry: all provider facts live as plain data in a single registry.ts file — no per-provider builder functions. Generic handlers in handlers.ts interpret the data to build MCP entries, sub-agent files, and rule frontmatter.
• Add Codex as the pilot end-to-end provider: TOML MCP config (.codex/config.toml), TOML subagent files (.codex/agents/*.toml), AGENTS.md instructions, rules-as-marker-blocks. Cursor and Claude Code integrations reproduce existing behavior byte-for-byte.
• Introduce the rules capabilities concept: a new top-level rules?: Rule[] field in capabilities.yaml. For providers with a dedicated rules directory (Cursor .cursor/rules/*.mdc), writes per-rule files with YAML frontmatter. For providers without one (Claude Code, Codex), folds rules into the instructions file as capa marker blocks.

New files

File	Purpose
src/types/providers.ts	ProviderIntegration, McpIntegration, InstructionsIntegration, RulesIntegration, SubagentsIntegration interfaces (data-only)
src/types/rules.ts	Rule interface
src/shared/providers/registry.ts	39-entry declarative provider registry with full Cursor/Claude Code/Codex integration data inlined
src/shared/providers/index.ts	Public API: getProvider(), getAllProviders(), getIntegratedProviders()
src/shared/providers/handlers.ts	Generic handlers: buildMcpEntry, buildSubAgentFile, buildRuleFrontmatter, getMcpConfigPath
src/shared/toml-io.ts	TOML read/write helpers (@iarna/toml)
src/cli/utils/rules-installer.ts	Install/clean rules across providers
src/shared/providers/__tests__/registry.test.ts	73 new tests

Modified files

• package.json — removed skills, added @iarna/toml
• src/cli/commands/install.ts — replaced skills imports, added Step 3.5 (rules)
• src/cli/commands/plugin-install.ts — replaced skills imports
• src/cli/commands/clean.ts — added rules cleanup
• src/cli/utils/mcp-client-manager.ts — registry-driven via handlers, JSON + TOML support
• src/cli/utils/agents-file.ts — registry-driven via buildSubAgentFile handler
• src/cli/utils/rules-installer.ts — registry-driven via buildRuleFrontmatter handler
• src/shared/plugin-manifest.ts — registry-driven manifest discovery
• src/types/capabilities.ts — added rules?: Rule[]

Test plan

• All 377 existing tests still pass (Cursor + Claude Code backward compatibility)
• 73 new tests cover registry parity (skillsDir/displayName for all 39 providers), pilot integrations, Codex MCP TOML round-trip, Codex subagent TOML generation, rules as marker blocks, Cursor rules as .mdc files
• Full suite: 450 pass, 0 fail

[Copilot]

Pull request overview

This PR replaces the external skills provider registry dependency with an in-repo “provider integration manifest” that becomes the single source of truth for provider-specific integration points (skills dirs, MCP config, instructions files, rules, subagents, plugin manifests). It also adds Codex as the pilot TOML-based provider and introduces a new cross-provider rules capability that can be installed either as per-rule files or folded into instructions via marker blocks.

Changes:

• Added declarative provider integration types + a 39-entry provider registry and generic handlers for MCP/subagents/rules generation.
• Added TOML read/write support and updated MCP registration to be registry-driven for both JSON and TOML clients (Codex).
• Introduced rules?: Rule[] in capabilities plus a rules installer/cleaner and corresponding tests.

Reviewed changes

Copilot reviewed 19 out of 20 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
src/types/rules.ts	Adds Rule type for new cross-provider rules capability.
src/types/providers.ts	Defines provider integration manifest interfaces (MCP/instructions/rules/subagents/plugins).
src/types/capabilities.ts	Adds rules?: Rule[] to capabilities and re-exports Rule.
src/shared/toml-io.ts	Adds TOML read/write + nested set/delete helpers for config edits.
src/shared/providers/registry.ts	Introduces the declarative provider registry (ported skills data + pilot integrations).
src/shared/providers/index.ts	Exposes provider lookup/listing APIs used across the CLI/shared code.
src/shared/providers/handlers.ts	Generic builders for MCP entries, subagent files, and rule frontmatter.
src/shared/providers/tests/registry.test.ts	Adds registry parity + pilot integration tests (Cursor/Claude/Codex/Copilot/Windsurf/etc.).
src/shared/plugin-manifest.ts	Makes plugin manifest discovery registry-driven (instead of hardcoded paths).
src/shared/capabilities.ts	Updates default capabilities structure (notably tools/security template changes).
src/shared/tests/capabilities.test.ts	Updates tests for the new default capabilities shape.
src/cli/utils/rules-installer.ts	Implements provider-aware rules installation/cleanup (files vs marker blocks).
src/cli/utils/mcp-client-manager.ts	Updates MCP registration/unregistration to use provider registry + TOML support.
src/cli/utils/agents-file.ts	Updates instructions/subagent generation to be registry-driven and adds provider-based target filenames.
src/cli/commands/plugin-install.ts	Removes skills dependency usage; installs skills using provider registry paths.
src/cli/commands/install.ts	Adds rules install step and switches skill install to provider registry.
src/cli/commands/clean.ts	Adds rules cleanup step during capa clean.
skills/capabilities-manager/SKILL.md	Updates documentation to reflect tool list removal from this skill.
package.json	Removes skills dependency and adds @iarna/toml.
bun.lock	Lockfile updates reflecting dependency changes.

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