Bugfix/tidyup makefile remove old targets

• Remove targets associated with old documentation

• Small fix for source file move

• Remove doxygen related content as migrated to FORD

• Remove out of date in file changelog.

• Make first time dependency generation a bit cleaner

• Make it easier to extend the cases in which we don't force the dependency file to be built

• Improve comment a bit

A collection of small fixes, tidying and convenience bits.