refactor: migrate data storage from JSON/map files to SQLite

Replace servers.json, certificates.json, and map file parsing with
SQLite (WAL mode) as single source of truth. HAProxy map files are
now generated from SQLite via sync_map_files().

Key changes:
- Add db.py with schema, connection management, and JSON migration
- Add DB_FILE config constant
- Delegate file_ops.py functions to db.py
- Refactor domains.py to use file_ops instead of direct list manipulation
- Fix subprocess.TimeoutExpired not caught (doesn't inherit TimeoutError)
- Add DB health check in health.py
- Init DB on startup in server.py and __main__.py
- Update all 359 tests to use SQLite-backed functions

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

haproxy_mcp/tools/certificates.py

@@ -1,6 +1,7 @@
 """Certificate management tools for HAProxy MCP Server."""
 
 import os
+import subprocess
 from datetime import datetime
 from typing import Annotated
 
@@ -152,7 +153,7 @@ def _haproxy_list_certs_impl() -> str:
                 certs.append(f"• {domain} ({ca})\n  Created: {created}\n  Renew: {renew}\n  Status: {status}")
 
         return "\n\n".join(certs) if certs else "No certificates found"
-    except TimeoutError:
+    except (TimeoutError, subprocess.TimeoutExpired):
         return "Error: Command timed out"
     except FileNotFoundError:
         return "Error: acme.sh not found"
@@ -203,7 +204,7 @@ def _haproxy_cert_info_impl(domain: str) -> str:
             result.stdout.strip()
         ]
         return "\n".join(info)
-    except TimeoutError:
+    except (TimeoutError, subprocess.TimeoutExpired):
         return "Error: Command timed out"
     except OSError as e:
         logger.error("Error getting certificate info for %s: %s", domain, e)
@@ -250,7 +251,7 @@ def _haproxy_issue_cert_impl(domain: str, wildcard: bool) -> str:
         else:
             return f"Certificate issued but PEM file not created. Check {host_path}"
 
-    except TimeoutError:
+    except (TimeoutError, subprocess.TimeoutExpired):
         return f"Error: Certificate issuance timed out after {CERT_TIMEOUT}s"
     except OSError as e:
         logger.error("Error issuing certificate for %s: %s", domain, e)
@@ -289,7 +290,7 @@ def _haproxy_renew_cert_impl(domain: str, force: bool) -> str:
         else:
             return f"Error renewing certificate:\n{output}"
 
-    except TimeoutError:
+    except (TimeoutError, subprocess.TimeoutExpired):
         return f"Error: Certificate renewal timed out after {CERT_TIMEOUT}s"
     except FileNotFoundError:
         return "Error: acme.sh not found"
@@ -323,7 +324,7 @@ def _haproxy_renew_all_certs_impl() -> str:
         else:
             return "Renewal check completed"
 
-    except TimeoutError:
+    except (TimeoutError, subprocess.TimeoutExpired):
         return "Error: Renewal cron timed out"
     except FileNotFoundError:
         return "Error: acme.sh not found"