Autoconf rebuilds all outputs files unnecessarily on #develop-neoloki

[josephnobes-stfc]

Relates to https://github.com/stfc-aeg/loki/tree/develop-neoloki

I attempted to write the config.mk file so that it would be possible to separate the autoconf-generated files into HW/SW/OS. The hope was that if for example the OS Makefile.in was modified, it would result in only the Makefile being regenerated by autoconf, and not also overwriting files in the HW tree (leading the the hardware makefile to consider the touched but unmodified files as new and therefore prompting a lengthly build).

Autoconf appears to have some caching ability, but in the way I've invoked it it either outputs all files or none of them, no matter if the input files related to specific output files have been modified.