Remove tracked binaries and fix build output directory (#248)

## Summary
- Remove registry binary from git tracking
- Update Makefile to output binaries to bin/ directory  
- Fix .gitignore to properly exclude bin/ directory and all binaries

This follows Go best practices by placing all compiled binaries in the
bin/ directory.

.gitignore

@@ -1,9 +1,9 @@
-build/*
+build/
+bin/
+
 .db
 .env
 .mcpregistry*
-**/bin
-cmd/registry/registry
 .DS_Store
 validate-examples
 validate-schemas