chore: Set clean version 0.5.9 for automated prerelease testing

- Revert to proper semantic version 0.5.9
- Sync manifest.json with clean version
- Prepare for make tag-dev automated prerelease generation

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <[email protected]>

Author: drernie

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "quilt-mcp-server"
-version = "0.5.9-rc.1"
+version = "0.5.9"
 description = "Secure MCP server for accessing Quilt data with JWT authentication"
 readme = "README.md"
 requires-python = ">=3.11"

tools/dxt/assets/manifest.json

@@ -1,7 +1,7 @@
 {
   "dxt_version": "0.1",
   "name": "quilt-mcp",
-  "version": "0.5.9-rc.1",
+  "version": "0.5.9",
   "description": "Access Quilt data packages through Claude Desktop",
   "author": {
     "name": "Quilt Data, Inc.",