That is why cleanup is both on shutdown and startup.
But that being said, i do not object to anyone creating a pull request or commit to store in temp directory. As long as they solve the reported problem. 
this multiple temporary lib caching stuff is resulting into breaking getClassLoader().getResource(…) since it creates a new temp directory on reloading a module which somehow results into an existing resource being looked up from a wrong place and thus file not being found. @dkayiwa where else are the api/src/main/resources files extracted/stored besides in this un-predictable cache folder from where fetching a resource results into File Not Found exception?
@k_joseph which openmrs platform version are you using?
1.11.2, i have this weirdly occurring on windows, i applied a hack that was very un-professional of me but worketh