Refactor server paths and add path override support

.github/workflows/bump-version.yml

@@ -67,11 +67,11 @@ jobs:
           jq ".version = \"${NEW_VERSION}\"" MCPForUnity/package.json > MCPForUnity/package.json.tmp
           mv MCPForUnity/package.json.tmp MCPForUnity/package.json
 
-          echo "Updating Server/pyproject.toml to $NEW_VERSION"
-          sed -i '0,/^version = ".*"/s//version = "'"$NEW_VERSION"'"/' "Server/pyproject.toml"
+          echo "Updating MCPForUnity/Server~/pyproject.toml to $NEW_VERSION"
+          sed -i '0,/^version = ".*"/s//version = "'"$NEW_VERSION"'"/' "MCPForUnity/Server~/pyproject.toml"
 
-          echo "Updating Server/README.md version references to v$NEW_VERSION"
-          sed -i 's|git+https://github.com/CoplayDev/unity-mcp@v[0-9]\+\.[0-9]\+\.[0-9]\+#subdirectory=Server|git+https://github.com/CoplayDev/unity-mcp@v'"$NEW_VERSION"'#subdirectory=Server|g' Server/README.md
+          echo "Updating MCPForUnity/Server~/README.md version references to v$NEW_VERSION"
+          sed -i 's|git+https://github.com/CoplayDev/unity-mcp@v[0-9]\+\.[0-9]\+\.[0-9]\+#subdirectory=MCPForUnity/Server~|git+https://github.com/CoplayDev/unity-mcp@v'"$NEW_VERSION"'#subdirectory=MCPForUnity/Server~|g' "MCPForUnity/Server~/README.md"
 
       - name: Commit and push changes
         env:
@@ -81,7 +81,7 @@ jobs:
           set -euo pipefail
           git config user.name "GitHub Actions"
           git config user.email "actions@github.com"
-          git add MCPForUnity/package.json "Server/pyproject.toml" Server/README.md
+          git add MCPForUnity/package.json "MCPForUnity/Server~/pyproject.toml" "MCPForUnity/Server~/README.md"
           if git diff --cached --quiet; then
             echo "No version changes to commit."
           else

.github/workflows/claude-mcp-preflight.yml

@@ -25,10 +25,10 @@ jobs:
           uv venv
           echo "VIRTUAL_ENV=$GITHUB_WORKSPACE/.venv" >> "$GITHUB_ENV"
           echo "$GITHUB_WORKSPACE/.venv/bin" >> "$GITHUB_PATH"
-          if [ -f Server/pyproject.toml ]; then
-            uv pip install -e Server
-          elif [ -f Server/requirements.txt ]; then
-            uv pip install -r Server/requirements.txt
+          if [ -f MCPForUnity/Server~/pyproject.toml ]; then
+            uv pip install -e "MCPForUnity/Server~"
+          elif [ -f MCPForUnity/Server~/requirements.txt ]; then
+            uv pip install -r MCPForUnity/Server~/requirements.txt
           else
             echo "No MCP Python deps found" >&2
             exit 1
@@ -48,8 +48,6 @@ jobs:
           cat > "$UNITY_MCP_STATUS_DIR/unity-mcp-status-dummy.json" <<JSON
           { "unity_port": 0, "reason": "dummy", "reloading": false, "project_path": "$UNITY_PROJECT_ROOT/Assets" }
           JSON
-          uv run --active --directory Server mcp-for-unity --transport stdio --help \
+          uv run --active --directory "MCPForUnity/Server~" mcp-for-unity --transport stdio --help \
             > /tmp/mcp-preflight.log 2>&1 || { cat /tmp/mcp-preflight.log; exit 1; }
           cat /tmp/mcp-preflight.log
-
-

.github/workflows/claude-nl-suite.yml

@@ -55,10 +55,10 @@ jobs:
           uv venv
           echo "VIRTUAL_ENV=$GITHUB_WORKSPACE/.venv" >> "$GITHUB_ENV"
           echo "$GITHUB_WORKSPACE/.venv/bin" >> "$GITHUB_PATH"
-          if [ -f Server/pyproject.toml ]; then
-            uv pip install -e Server
-          elif [ -f Server/requirements.txt ]; then
-            uv pip install -r Server/requirements.txt
+          if [ -f MCPForUnity/Server~/pyproject.toml ]; then
+            uv pip install -e "MCPForUnity/Server~"
+          elif [ -f MCPForUnity/Server~/requirements.txt ]; then
+            uv pip install -r MCPForUnity/Server~/requirements.txt
           else
             echo "No MCP Python deps found (skipping)"
           fi
@@ -409,7 +409,7 @@ jobs:
                           "run",
                           "--active",
                           "--directory",
-                          "Server",
+                          "MCPForUnity/Server~",
                           "mcp-for-unity",
                           "--transport",
                           "stdio",
@@ -512,7 +512,7 @@ jobs:
           attempt=0
           while true; do
             attempt=$((attempt+1))
-            if uv run --active --directory Server mcp-for-unity --transport stdio --help > /tmp/mcp-preflight.log 2>&1; then
+            if uv run --active --directory "MCPForUnity/Server~" mcp-for-unity --transport stdio --help > /tmp/mcp-preflight.log 2>&1; then
               cat /tmp/mcp-preflight.log
               break
             fi
@@ -541,7 +541,7 @@ jobs:
           echo "--- PortDiscovery debug ---"
           python3 - <<'PY'
           import sys
-          sys.path.insert(0, "Server/src")
+          sys.path.insert(0, "MCPForUnity/Server~/src")
           from transport.legacy.port_discovery import PortDiscovery
           import json
 
@@ -556,7 +556,7 @@ jobs:
           import json
           import subprocess
           cmd = [
-              "uv", "run", "--active", "--directory", "Server", "python", "-c",
+              "uv", "run", "--active", "--directory", "MCPForUnity/Server~", "python", "-c",
               "from transport.legacy.stdio_port_registry import stdio_port_registry; "
               "inst = stdio_port_registry.get_instances(force_refresh=True); "
               "import json; print(json.dumps([{'id':i.id,'port':i.port} for i in inst]))"
@@ -577,7 +577,7 @@ jobs:
           PY
 
           echo "=== Testing MCP server startup with --status-dir flag ==="
-          uv run --active --directory Server python <<'PYTEST'
+          uv run --active --directory "MCPForUnity/Server~" python <<'PYTEST'
           import os
           import sys
           import glob
@@ -602,7 +602,7 @@ jobs:
           set -euxo pipefail
           echo "=== Unity container status ==="
           docker inspect -f '{{.State.Status}} {{.State.Running}}' unity-mcp || echo "Container not found!"
-          
+
           echo "=== Raw socket probe to Unity ==="
           # Try raw TCP connect without Python overhead
           for host in 127.0.0.1 localhost; do
@@ -613,10 +613,10 @@ jobs:
               echo "$host:6400 - FAILED"
             fi
           done
-          
+
           echo "=== Netstat for port 6400 ==="
           docker exec unity-mcp netstat -tlnp 2>/dev/null | grep 6400 || ss -tlnp | grep 6400 || echo "No listener found on 6400"
-          
+
           echo "=== Python probe with timing ==="
           python3 <<'PY'
           import socket, time

.github/workflows/python-tests.yml

@@ -4,7 +4,7 @@ on:
   push:
     branches: ["**"]
     paths:
-      - Server/**
+      - MCPForUnity/Server~/**
       - .github/workflows/python-tests.yml
   workflow_dispatch: {}
 
@@ -22,17 +22,17 @@ jobs:
           version: "latest"
 
       - name: Set up Python
-        run: uv python install 3.10
+        run: uv python install 3.11
 
       - name: Install dependencies
         run: |
-          cd Server
+          cd MCPForUnity/Server~
           uv sync
           uv pip install -e ".[dev]"
 
       - name: Run tests
         run: |
-          cd Server
+          cd MCPForUnity/Server~
           uv run pytest tests/ -v --tb=short
 
       - name: Upload test results
@@ -41,5 +41,5 @@ jobs:
         with:
           name: pytest-results
           path: |
-            Server/.pytest_cache/
-            Server/tests/
+            MCPForUnity/Server~/.pytest_cache/
+            MCPForUnity/Server~/tests/