When building my app with a build of latest emsdk 3.1.69, I found that the virtual file system would no longer be populated and only contained the bare hardcoded minimum. Turned out that

commit 483cdcd5306780520a2de8856fcd13910e71497e
Author: Sam Clegg <[email protected]>
Date:   Thu Oct 3 14:35:51 2024 -0700

    Micro-optimize preRun/postRun handling. NFC (#22671)
[...]
diff --git a/src/preamble.js b/src/preamble.js
index d37cb9fe7..3a6aee9c9 100644
--- a/src/preamble.js
+++ b/src/preamble.js
@@ -195,11 +195,10 @@ function preRun() {
   assert(!ENVIRONMENT_IS_PTHREAD); // PThreads reuse the runtime from the main 
thread.
 #endif
 #if expectToReceiveOnModule('preRun')
-  if (Module['preRun']) {
-    if (typeof Module['preRun'] == 'function') Module['preRun'] = 
[Module['preRun']];
-    while (Module['preRun'].length) {
-      addOnPreRun(Module['preRun'].shift());
-    }
+  var preRuns = Module['preRun'];
+  if (preRuns) {
+    if (typeof preRuns == 'function') preRuns = [preRuns];
+    preRuns.forEach(addOnPreRun);
   }
 #endif
   callRuntimeCallbacks(__ATPRERUN__);
[...]

caused the function runWithFS to no longer be called, because it gets added to Module.preRun from within the function runMetaWithFS that itself is called from within the function preRun.

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