Verify the integrated application and complete the migration

docs/operations.md

@@ -37,7 +37,7 @@ output files elsewhere.
 
 ## Diagnostics Directory
 
-The [diagnostics configuration](config.md#thresholds-context-and-diagnostics)
+The [diagnostics configuration](config.md#settings)
 selects the parent work directory. Runs create children named like
 `run-<unix-nanoseconds>`. The runtime creates the work directory if needed.
 Report paths may be relative when the supplied work directory is relative;
@@ -68,7 +68,7 @@ write succeeded or that the files still exist after retention.
 
 ## Retention Behavior
 
-[Configuration](config.md#thresholds-context-and-diagnostics) owns accepted
+[Configuration](config.md#settings) owns accepted
 retention values and the default. Current lifecycle behavior is:
 
 | Run outcome / selection | Directory outcome |
@@ -89,10 +89,10 @@ Run artifacts can contain full transcripts, glossary-related context, and LLM
 prompts/responses. Configured-key redaction does not anonymize those contents.
 Choose a work directory whose ownership and permissions fit the transcript data,
 and retain or share artifacts intentionally. Credential-supply mechanisms are
-owned by [configuration](config.md#secrets).
+owned by [configuration](config.md#credentials).
 
 For a debugging run, select retained diagnostics using the
-[retention flag](cli.md#process-flag-reference). Copy needed artifacts before
+[retention flag](cli.md#setting-overrides). Copy needed artifacts before
 removing completed run directories manually. Avoid deleting a directory while
 its run is active. Audita does not provide a separate archival/backup or remote
 artifact storage facility.