feat: upgrade to Agent OS Enhanced and version 0.1.0rc3

Major upgrade combining MCP server modernization, version refactoring,
and Agent OS Enhanced integration.

## MCP Server: Prototype → Product (mcp_servers → mcp_server)

Upgraded from prototype MCP server to modular Agent OS Enhanced architecture:

**New Modular Structure:**
- config/ - Configuration loading and validation
- core/ - Dynamic registry, parsers, session management
- server/ - FastMCP server factory and tool registration
- models/ - Pydantic models for config, RAG, workflows
- monitoring/ - File watcher for auto-indexing

**New Capabilities:**
- Workflow engine with phase gating and evidence validation
- Framework generator for creating new workflows
- File watcher for incremental RAG index updates
- Comprehensive workflow tooling (start, complete phase, get state)
- Enhanced RAG tools with standards/usage/workflows indexing

**Removed Prototype:**
- Deleted old mcp_servers/ implementation (1,999 lines)
- Removed run_mcp_server.py entry point
- Moved tests to upstream agent-os-enhanced repo (-2,326 lines)

## Version Refactoring: Single Source of Truth

Consolidated version definition from 5 hardcoded locations to 1:

**Before:** Version hardcoded in 5 files (src + tests)
**After:** Version defined once in __init__.py, imported everywhere

**Changes:**
- src/honeyhive/__init__.py: Define __version__ at top (before imports)
- src/honeyhive/api/client.py: Import and use __version__ for User-Agent
- src/honeyhive/tracer/processing/context.py: Import and use for tracer metadata
- tests/: Updated 4 test files to use dynamic version assertions

**Benefits:**
- 80% reduction in update effort (1 file vs 5 files)
- Eliminates risk of version inconsistency
- Follows standard Python practices

## Agent OS Enhanced Content

Added universal Agent OS content for AI-assisted workflows:

**Usage Guides (5 files, 2,306 lines):**
- operating-model.md - AI authorship vs human orchestration model
- mcp-usage-guide.md - How to use MCP tools effectively
- mcp-server-update-guide.md - Server update procedures
- agent-os-update-guide.md - Content sync procedures
- creating-specs.md - Specification-driven development guide

**Workflows (9 files, 1,929 lines):**
- spec_execution_v1/ - Specification execution workflow framework
  - metadata.json - Workflow configuration and phase definitions
  - phases/0/ - Discovery phase (locate spec, parse tasks, build plan)
  - phases/dynamic/ - Templates for dynamic task execution
  - core/ - Task parser, dependency resolver, validation gates

## Configuration & Build Updates

- .cursor/mcp.json: Updated to use modular server with isolated venv
- .agent-os/scripts/build_rag_index.py: Fixed paths for python-sdk structure
- .agent-os/mcp_server/requirements.txt: Added fastmcp>=2.0.0

## Test Cleanup

- Removed tests/unit/mcp_servers/ (6 files, 2,326 lines)
- Rationale: MCP server tests now maintained in upstream agent-os-enhanced
- Fixed unused argument warnings in tracer tests (6 lines)

## Quality Metrics

✅ Format: 270 files clean
✅ Lint: 10.00/10 (up from 9.99)
✅ Unit Tests: 2,802 passing, 88.07% coverage
✅ Integration: 153/154 passing (1 flaky timing test)

## Impact

68 files changed
+10,741 insertions
-4,721 deletions
Net: +6,020 lines

**Distribution:**
- MCP server upgrade: +5,823 lines
- Agent OS content: +4,235 lines
- Version refactoring: +31 lines (net)
- Test cleanup: -2,326 lines
- Prototype removal: -1,999 lines

## Breaking Changes

**MCP Server Entry Point Changed:**
Old: `python .agent-os/run_mcp_server.py`
New: `python -m mcp_server` (with PYTHONPATH=.agent-os)

**Directory Structure Changed:**
Old: `.agent-os/mcp_servers/` (plural)
New: `.agent-os/mcp_server/` (singular, modular)

**Required Directory Structure:**
Projects now require `.agent-os/usage/` and `.agent-os/workflows/` directories
for proper MCP server configuration validation.

## Upgrade Notes

1. Cursor will automatically use new MCP server via updated .cursor/mcp.json
2. RAG index rebuilt with 5,164 chunks (standards + usage + workflows)
3. Version updates now only require editing src/honeyhive/__init__.py
4. MCP server runs in isolated venv at .agent-os/venv/

Co-authored-by: Agent OS Enhanced <agent-os@honeyhive.ai>
