Are there any tools out there to keep track of which works you have already defined, managing your lexicon easily, and storing conjugations and the like?
Barring that, what are some good strategies to keep everything organized in text files?
Polyglot is a piece of software made specifically for the organisation, and management of conlangs as a whole. I haven't used it personally (preferring pen and paper to a large extent), but I've heard a fair few positive things about it.
Conworkshop includes a bunch of different tools for storing and organising things, but I've personally not found it particularly useful, and I have heard from people who have looked at the backend that you do not want to look at the backend, though I think they are doing a rewrite.
SIL Fieldworks is a vocabulary management program, and while developed for natlang lexicographers, it's also useful for conlangs. It's a rather powerful tool, but it has a significant learning curve to it. SIL also publishes other potentially useful free software such as Toolbox: https://software.sil.org/products/
Lexique Pro is a piece of software for making and editing presentable dictionaries. I haven't used it but it apparently offers compatibility with Fieldworks.
In addition to these, a regular spreadsheet program and a text editor can be quite useful, and there is a sea of both web and downloadable word generators (e.g. Gen, Awkwords, Lexifer) and sound change appliers (e.g. SCA2, GSCA), and for writing publishable materials, LaTeX, combined with a variety of packages for extra functionality such as Lingmacros and TikZ can produce fantastic results.
Personally, I use (Xe)LaTeX, as well as a Perl6 script to convert a custom-made dictionary format into LaTeX markup. Don't really need anything else, other than the occasional pen and paper for jotting down ideas.
You could also do everything on paper as Isoraķatheð does.