diff --git a/messages/run-command.md b/messages/run-command.md
index 1117844b7..443acea81 100644
--- a/messages/run-command.md
+++ b/messages/run-command.md
@@ -142,6 +142,13 @@ To output the results to multiple files, specify this flag multiple times. For e
 
 If you specify a file within a folder, such as `--output-file ./out/results.json`, the folder must already exist, or you get an error. If the file already exists, it's overwritten without prompting.
 
+<!-- sfge threading flags removed; configuration now lives purely in yaml -->
+
+> **Note:** SFGE engine threading settings are no longer exposed as CLI
+> flags.  Please configure `engines.sfge.java_thread_count` and
+> `engines.sfge.java_thread_timeout` in your `code-analyzer.yml`/`.yaml`
+> file.  The CLI will automatically pick up values from that file when it is
+> present.
 # error.invalid-severity-threshold
 
 Expected --severity-threshold=%s to be one of: %s
diff --git a/src/commands/code-analyzer/run.ts b/src/commands/code-analyzer/run.ts
index ff3773332..bc228c8b1 100644
--- a/src/commands/code-analyzer/run.ts
+++ b/src/commands/code-analyzer/run.ts
@@ -70,7 +70,12 @@ export default class RunCommand extends SfCommand<void> implements Displayable {
 			description: getMessage(BundleName.RunCommand, 'flags.config-file.description'),
 			char: 'c',
 			exists: true
-		})
+		}),
+		// === Flags pertaining to SFGE engine tuning ===
+		// NOTE: thread count/timeout are now configured via the YAML file
+		// (engines.sfge.java_thread_count / engines.sfge.java_thread_timeout) and
+		// are no longer exposed as CLI flags. Keeping the section around so the
+		// comment about configuration is still surfaced in help text.
 	};
 
 	public async run(): Promise<void> {
@@ -84,8 +89,11 @@ export default class RunCommand extends SfCommand<void> implements Displayable {
 			'workspace': parsedFlags['workspace'],
 			'severity-threshold': parsedFlags['severity-threshold'] === undefined ? undefined :
 				convertThresholdToEnum(parsedFlags['severity-threshold'].toLowerCase()),
-			'target': parsedFlags['target']
+'target': parsedFlags['target']
 		};
+		// sfge threading parameters are controlled entirely through the config
+		// file now; the CLI used to accept overrides but those flags have been
+		// removed.
 		await action.execute(runInput);
 	}
 
diff --git a/src/lib/actions/RunAction.ts b/src/lib/actions/RunAction.ts
index 510620c3d..8248eb3cf 100644
--- a/src/lib/actions/RunAction.ts
+++ b/src/lib/actions/RunAction.ts
@@ -40,7 +40,6 @@ export type RunInput = {
 	'severity-threshold'?: SeverityLevel;
 	target?: string[];
 	workspace: string[];
-
 }
 
 export class RunAction {
@@ -51,6 +50,10 @@ export class RunAction {
 	}
 
 	public async execute(input: RunInput): Promise<void> {
+		// Threading configuration for the SFGE engine is now solely managed via the
+		// user’s YAML configuration file (engines.sfge.java_thread_count and
+		// engines.sfge.java_thread_timeout).  CLI overrides were removed, so we
+		// simply forward the config file path to the factory.
 		const config: CodeAnalyzerConfig = this.dependencies.configFactory.create(input['config-file']);
 		const logWriter: LogFileWriter = await LogFileWriter.fromConfig(config);
 		this.dependencies.actionSummaryViewer.viewPreExecutionSummary(logWriter.getLogDestination());