Use glossaries package

[clbarnes]

As referred to in #34 .

Glossaries is incompatible with the index option in \documentclass, but may also make it obsolete if you choose not to use the nonumberlist option of glossaries (I have used it here because I think the numbers look messy).

The updates to the bash script seem to work but I can't test the changes to the .bat file (although they're very simple).

The updates to the make file seem to work for my use case (just running the default target), but are a bit gross.

[clbarnes]

I'm not sure how to get the Makefile to clean up thesis.acn, thesis.acr, and thesis.alg. I tried

.PHONY: clean-gls
clean-gls:
	%(QUIET)$(call clean-files,$(graph_stem) *.acn *.acr *.alg)

.PHONY: clean
clean: clean-generated clean-tex clean-graphics clean-deps clean-backups clean-auxiliary clean-gls ;

but get

%(QUIET)rm -f thesis.acn thesis.acr thesis.alg
/bin/sh: 1: Syntax error: word unexpected (expecting ")")
Makefile:3529: recipe for target 'clean-gls' failed
make: *** [clean-gls] Error 2

I expect it's a simple solution which you may be better equipped to drop in.

The bash and bat scripts now do clean those files.