[ddev] Atomic config swap to avoid autodiscovery deregister race

The `--config-file` path of `ddev env agent` previously renamed the original
config away before writing the override, leaving a window in which the
mounted conf.d directory had no config for the integration. Agent
autodiscovery rescans on file events; if it scanned during that window it
deregistered the check, and the immediately-following `agent check <name>`
returned "no valid check found".

This is the actual SNMP master.yml flake fingerprint: agent runs cleanly for
10+ minutes (20-30 successful check cycles), then a single test using
`dd_agent_check` (which goes through this code path) hits the race and
fails. Two of the last three master.yml SNMP failures match it exactly.

Switch to read-modify-restore in place. `EnvData.write_config` now writes
via tmp + os.replace so the file is never transiently absent.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

Author: Kyle-Neale

ddev/src/ddev/cli/env/agent.py

@@ -71,10 +71,15 @@ def agent(app: Application, *, intg_name: str, environment: str, args: tuple[str
         finally:
             env_data.config_file.unlink()
     else:
-        temp_config_file = env_data.config_file.parent / f'{env_data.config_file.name}.bak.example'
-        env_data.config_file.replace(temp_config_file)
+        # Read-modify-restore in place. The previous implementation renamed
+        # the original config away before writing the override, which left a
+        # window where the conf.d directory contained no config for this
+        # integration; if Agent autodiscovery rescanned during that window it
+        # deregistered the check and the immediately-following `agent check`
+        # returned "no valid check found".
+        original_config = env_data.read_config()
         try:
             env_data.write_config(config)
             agent.invoke(full_args)
         finally:
-            temp_config_file.replace(env_data.config_file)
+            env_data.write_config(original_config)

ddev/src/ddev/e2e/config.py

@@ -42,13 +42,21 @@ def write_config(self, config: dict[str, Any] | None) -> None:
         if config is None:
             return
 
+        import os
+
         import yaml
 
         if 'instances' not in config:
             config = {'instances': [config]}
 
         self.config_file.parent.ensure_dir_exists()
-        self.config_file.write_text(yaml.safe_dump(config, default_flow_style=False))
+        # Write via tmp + os.replace so the file is never transiently absent.
+        # Agent autodiscovery watches this directory; if it observes the path
+        # missing it deregisters the integration's check, causing later
+        # `agent check <name>` invocations to fail with "no valid check found".
+        tmp = self.config_file.parent / f'.{self.config_file.name}.swap'
+        tmp.write_text(yaml.safe_dump(config, default_flow_style=False))
+        os.replace(tmp, self.config_file)
 
     def read_metadata(self) -> dict[str, Any]:
         import json