Tectonic does not handle everything yet, unfortunately. I am guessing the same holds for your glossary and acronyms. So, same holds as with biber: how do you build the glossary and acronyms locally? (I’m not going to dig through your thesis to find that out). Then do the same on Travis.
If you believe Tectonic should support this, check for issues at https://github.com/tectonic-typesetting/tectonic/issues or create one yourself (including sufficient information about how you are building your glossary/acronyms).
I use TexStudio for building the project. Sadly I have no idea how it builds the glossary or which commands it executes to build it. I will try to find it by googling. Thank you PHPirates!
Update:
I found this shell commands in the manual of the glossaries package: