The clean command has to be usually run before running the auto command. If the previous compilation has failed, then running auto will just hang. In this case I have to run clean and then auto, which is quite frequently.
Will it make sense to automatically trigger the clean when the auto command is run ?
I have not found this to be the case. The auto command is pretty simple; it just looks at the output file timestamp, and rebuilds things if the output file is older than any of the input files. So, sometimes you will start auto mode and nothing will be built until you touch a source file, because according to the timestamps nothing needs to be done.
If there is a case where the output file's timestamp is older than an input file's timestamp, and auto does not perform a build, then that is indeed a bug, but you'll need to provide a reproduction case to prove that it's happening before it will be fixable.
I'm not sure this is related, but you might want to look at http://dev.clojure.org/jira/browse/CLJS-282 . It could be involved with whatever problems you're having.
Closing due to no reproduction case.