Comment made by: thheller
FWIW I added support for this in shadow-build a while ago. It does not need inline source maps to work.
The code can be found here: https://github.com/thheller/shadow-build/blob/master/src/main/shadow/cljs/closure.clj
The relevant bits are {{.addInputSourceMap}} on {{Compiler}} and {{.setApplyInputSourceMaps}} on {{CompilerOptions}}.
If everything is properly configured the warnings displayed by Closure will contain an "Originally at:" location which points to the CLJS file.
Closure will also use the input source maps when generating source maps for {{:advanced}} builds, so the manual merge done by CLJS at the moment becomes unnecessary. The source maps also appear to be more accurate. Before input source maps I had a few issues where source maps were off by a few lines, but that may have been due to my incorrect source map handling in shadow-build.