refactor: rename plugin to skill terminology

[bug-ops]

Summary

This PR renames all "plugin" terminology to "skill" throughout the codebase to align with Anthropic's official MCP Code Execution specification.

Rationale: ADR-007 documents that Anthropic explicitly uses "Skills" (not "Plugins") for the code execution pattern. Skills are distinct from traditional plugins through their filesystem-based progressive disclosure approach.

Changes

🏗️ Core Refactoring

• Renamed crate: mcp-plugin-store → mcp-skill-store
• Renamed types: PluginStore → SkillStore, PluginMetadata → SkillMetadata, etc.
• Renamed CLI commands: mcp-cli plugin → mcp-cli skill
• Updated default paths: ./plugins → ./skills

📚 Documentation

• ADR-007: New ADR documenting the terminology alignment
• ADR-006: Renamed and updated from plugin-persistence to skill-persistence
• Module docs: All comments and documentation updated
• Examples: All code examples use skill terminology

🧪 Testing & Quality

• ✅ 758 tests passing (100%)
• ✅ 317 doc tests passing (100%)
• ✅ Clippy clean (no warnings)
• ✅ All benchmarks updated and passing

Files Changed

19 files changed, 1,937 insertions(+), 874 deletions(-)

Critical Files:

• crates/mcp-skill-store/ (entire crate renamed)
• crates/mcp-cli/src/commands/skill.rs (renamed from plugin.rs)
• crates/mcp-cli/src/main.rs (CLI command enum updated)
• Cargo.toml (workspace member renamed)
• docs/adr/006-skill-persistence.md (renamed and updated)
• docs/adr/007-skill-terminology-alignment.md (new)

Breaking Changes

⚠️ This is a breaking change:

CLI:

# Before:
mcp-cli plugin list
mcp-cli plugin load my-server

# After:
mcp-cli skill list
mcp-cli skill load my-server

API:

// Before:
use mcp_plugin_store::{PluginStore, PluginMetadata};
let store = PluginStore::new("./plugins")?;

// After:
use mcp_skill_store::{SkillStore, SkillMetadata};
let store = SkillStore::new("./skills")?;

Default paths:

• Old: ./plugins/
• New: ./skills/

Migration Guide

1. Update imports:

   - use mcp_plugin_store::{PluginStore, PluginMetadata};
   + use mcp_skill_store::{SkillStore, SkillMetadata};

2. Rename directories:

   mv ./plugins ./skills

3. Update CLI commands:

   # All plugin subcommands → skill subcommands
   mcp-cli skill list

Related

• ADR-007: Skill Terminology Alignment with Anthropic Specification
• ADR-006: Skill Persistence Design (updated)
• Anthropic Article: https://www.anthropic.com/engineering/code-execution-with-mcp

Testing

Comprehensive testing performed:

• ✅ Unit tests (758 passing)
• ✅ Integration tests (all passing)
• ✅ Doc tests (317 passing)
• ✅ Benchmarks (all building and running)
• ✅ Code review completed

Checklist

• All tests passing
• Clippy clean
• Documentation updated
• ADR created
• Breaking changes documented
• Migration guide provided
• Code review completed
• Git history preserved (used git mv)

[codecov-commenter]

Codecov Report

❌ Patch coverage is 95.81152% with 8 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
crates/mcp-skill-store/src/store.rs	94.83%	8 Missing ⚠️

@@            Coverage Diff             @@
##           master       #9      +/-   ##
==========================================
- Coverage   92.31%   92.30%   -0.01%     
==========================================
  Files          29       29              
  Lines        4968     4966       -2     
==========================================
- Hits         4586     4584       -2     
  Misses        382      382              

Flag	Coverage Δ
unittests	92.30% <95.81%> (-0.01%)	⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files with missing lines	Coverage Δ
crates/mcp-skill-store/src/checksum.rs	98.02% <100.00%> (ø)
crates/mcp-skill-store/src/error.rs	100.00% <100.00%> (ø)
crates/mcp-skill-store/src/types.rs	100.00% <100.00%> (ø)
crates/mcp-skill-store/src/store.rs	94.01% <94.83%> (ø)

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