diff --git a/js/grunt/tasks/output-js-project.ts b/js/grunt/tasks/output-js-project.ts
index c1f3d691..5be4b80c 100644
--- a/js/grunt/tasks/output-js-project.ts
+++ b/js/grunt/tasks/output-js-project.ts
@@ -6,8 +6,11 @@ import transpile, { getTranspileOptions } from '../transpile.js';
 
 /**
  * Outputs JS for the specified repo and its dependencies
- * TODO: We need output-js-project because of maintenance tooling, but should we add a duplicate for `transpile-project`? https://github.com/phetsims/chipper/issues/1499
- * TODO: output-js-project --watch does not work. Transpiler.watch() hard codes active repos (let's wait to fix for swc), https://github.com/phetsims/chipper/issues/1499
+ *
+ * NOTE: We need to keep the name output-js-project because of maintenance tooling. This name should never change,
+ * though SR and MK wish it was called "transpile-project".
+ *
+ * TODO: output-js-project --watch does not work. Transpiler.watch() hard codes active repos (let's wait to fix for swc), https://github.com/phetsims/chipper/issues/1354
  * @author Sam Reid (PhET Interactive Simulations)
  * @author Michael Kauzmann (PhET Interactive Simulations)
  */
diff --git a/js/grunt/tasks/output-js.ts b/js/grunt/tasks/output-js.ts
index 89179bf1..d7c5784c 100644
--- a/js/grunt/tasks/output-js.ts
+++ b/js/grunt/tasks/output-js.ts
@@ -5,8 +5,7 @@ import transpile, { getTranspileOptions } from '../transpile.js';
 /**
  * Main entrypoint for transpiling the PhET codebase to js. See transpile() for API. Outputs JS just
  * for the specified repo by default.
- * TODO: Can we rename this to "transpile", it is ok that we keep output-js-project for backwards compatibility. https://github.com/phetsims/chipper/issues/1499
- *
+ * TODO: Rename this to "transpile", it is ok that we keep output-js-project for backwards compatibility. https://github.com/phetsims/chipper/issues/1499
  *
  * @author Sam Reid (PhET Interactive Simulations)
  */
diff --git a/js/grunt/transpile.ts b/js/grunt/transpile.ts
index 09a04124..4acc0ab9 100644
--- a/js/grunt/transpile.ts
+++ b/js/grunt/transpile.ts
@@ -99,7 +99,7 @@ Watching...
   else {
     // TODO: update doc about running transpiler that doesn't include `--repos` (use output-js-project --watch), https://github.com/phetsims/chipper/issues/1499
     //       https://github.com/phetsims/phet-info/blob/main/doc/phet-development-overview.md#creating-a-new-sim
-    // TODO: The above doesn't work. Do we need to support this before upgrading to swc? https://github.com/phetsims/chipper/issues/1499
+    // TODO: The above doesn't work. Do we need to support this before upgrading to swc? https://github.com/phetsims/chipper/issues/1354
     transpiler.transpileRepos( _.uniq( options.repos ) );
   }
 
diff --git a/js/scripts/transpile.js b/js/scripts/transpile.js
index 053f0cb1..900f15de 100644
--- a/js/scripts/transpile.js
+++ b/js/scripts/transpile.js
@@ -1,6 +1,7 @@
 // Copyright 2021-2024, University of Colorado Boulder
 
 /**
+ * @deprecated - use `grunt output-js --watch`.
  * Command Line Interface (CLI) for TypeScript transpilation via babel.  Transpiles *.ts and copies all *.js files to
  * chipper/dist/js. Does not do type checking. Filters based on active-repos and subsets of directories within repos
  * (such as js/, images/, and sounds/)