revert: remove file-based configuration and multi-spec support

This reverts commit 9185b5fa05 while
preserving the build work done afterwards: setuptools-scm versioning with
uv cache keys, the git-enabled Docker builder (full checkout, credentials
excluded), and full-history/tag checkout in CI.

Configuration returns to environment variables with a single OpenAPI
document; .env.example and the env-based Docker/Compose setup are
restored.

Dockerfile

@@ -32,11 +32,13 @@ FROM python:3.14-alpine3.24 AS runtime
 
 ENV PYTHONDONTWRITEBYTECODE=1 \
     PYTHONUNBUFFERED=1 \
-    PATH="/app/.venv/bin:$PATH"
+    PATH="/app/.venv/bin:$PATH" \
+    MCP_TRANSPORT=http \
+    MCP_HOST=0.0.0.0 \
+    MCP_PORT=8000
 
 RUN addgroup -S -g 1001 xmcp \
- && adduser -S -D -H -u 1001 -G xmcp xmcp \
- && mkdir -p /etc/xmcp
+ && adduser -S -D -H -u 1001 -G xmcp xmcp
 
 WORKDIR /app
 COPY --from=builder --chown=xmcp:xmcp /app/.venv /app/.venv
@@ -45,8 +47,8 @@ USER xmcp
 
 EXPOSE 8000
 
-# Probes the MCP HTTP port when the mounted configuration uses transport http.
+# In HTTP mode, probe the MCP port; stdio containers are always healthy.
 HEALTHCHECK --interval=30s --timeout=5s --start-period=10s --retries=3 \
-    CMD ["python", "-m", "xmcp.healthcheck"]
+    CMD ["python", "-c", "import os, socket, sys\nif os.environ.get('MCP_TRANSPORT', 'stdio') != 'http':\n    sys.exit(0)\ns = socket.socket()\ns.settimeout(3)\nsys.exit(s.connect_ex(('127.0.0.1', int(os.environ.get('MCP_PORT', '8000')))))"]
 
 CMD ["python", "-m", "xmcp"]