fix: version string inconsistencies across codebase

[BryanFRD]

Describe the bug
The package is at v3.2.0 but version strings are inconsistent:

Location	Version
package.json	3.2.0
src/index.ts (MCP server version)	1.1.0
src/tools/api-client.ts (User-Agent)	ferrflow-mcp/0.2.0
src/tools/github.ts line 56 (User-Agent)	ferrflow-mcp/0.2.0
src/tools/github.ts line 99 (User-Agent)	ferrflow-mcp/0.3.1

Package
Which package is affected? [x] server [x] tools [ ] docs

To Reproduce
Not provided in the original issue — to be filled in.

Expected behavior
Proposed fix:

• Read version from package.json at runtime or use a shared constant
• Update all User-Agent strings to match the package version
• Update the MCP server version in index.ts

Environment

• Package version: main
• Browser/OS (if frontend): n/a