Fix: Expose only serena scripts in Nix package, exclude Python interpreter (#753)

* Fix: Expose only serena scripts in Nix package, exclude Python interpreter

Modified flake.nix to use a wrapper derivation that filters the virtual
environment to expose only serena-specific executables (serena, serena-mcp-server,
index-project) while excluding the Python interpreter and other venv binaries.

The full virtual environment is still accessible via 'nix build .#serena-env'
for development purposes.

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

Co-Authored-By: Claude <noreply@anthropic.com>

* Remove deprecated commands from Nix package exports

This change removes serena-mcp-server and index-project from the default
Nix package outputs, exposing only the serena command. These commands are
deprecated and will be removed soon, so they should not be part of the
public package interface.

Addresses PR review feedback requesting to expose only the serena command.

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

Co-Authored-By: Claude <noreply@anthropic.com>

---------

Co-authored-by: Claude <noreply@anthropic.com>

flake.nix

@@ -76,7 +76,11 @@
       formatter = pkgs.alejandra;
 
       packages = {
-        serena = pythonSet.mkVirtualEnv "serena" workspace.deps.default;
+        serena-env = pythonSet.mkVirtualEnv "serena-env" workspace.deps.default;
+        serena = pkgs.runCommand "serena" {} ''
+          mkdir -p $out/bin
+          ln -s ${packages.serena-env}/bin/serena $out/bin/serena
+        '';
         default = packages.serena;
       };