Should I preserve anonymity or strictly follow a journal's instructions? I'm submitting a manuscript to a journal using LaTeX for the first time. This journal is a little unique in that it features open source software packages, and you must provide a link to a public repository upon submission. It has a .tex template that I've filled in, but I'm a little confused about how to preserve anonymity for the sake of blind review. A reviewer could easily identify me based on 


My GitHub profile info
My name embedded in the .tex file (obviously)
Info in the acknowledgements section


It would be easy for a journal to programmatically remove sections with identifying information from this .tex template (such as author name, acknowledgements section, etc.), but I doubt this is done. Also, I have to submit a .pdf (rendered from the .tex file) along with the .tex file of my actual document. I'm a little confused about preserving anonymity vs. following the instructions of journal, as these seem clear that the template should be filled in exactly as is with no deviations. Is is just understood that that all potentially identifying information should be removed from a first submission, even if it means breaking (what seems to be) a journal's clear instructions? Or am I misunderstanding how this all works?

To provide extra context from a past experience (not directly related to the case mentioned above):

I've only submitted one other manuscript to a journal, and the initial process involved heavy assistance from my advisor (subsequent steps were taken on my own). The editor of the journal requested that I revise and resubmit, following an attached style guide. It was a 60+ page document with pretty arcane instructions containing a lot of counter-intuitive information. For example, it stated that the authors' names must be included as a footnote on every page (which would break anonymity), an acknowledgements section should be embedded inside the document (which could reveal identifying information such as location), etc. I asked the editor about this, and he was very helpful. He provided some specific instructions and stated that anonymity should be persevered throughout the document -- I think he was more concerned with reference formatting. However, this was a really confusing process as his instructions seemed to go against the "Instructions for Authors" guide and the style sheet he attached. To make things worse, the actual submission page conflicted with the "Instructions for Authors" guide and the style sheet. I did what the editor said.

My sample size is small (n = 2), but given the two manuscript submissions I've been through, it seems like either (a) I'm making a big deal out of nothing or (b) I'm really misunderstanding things.
Follow the instructions. If you do it wrong, the journal will send it back to you with a grumpy note. Some journals do not practice double blind review but rather single blind, so the authors are known but the reviewers are anonymous. (Discussing the merits and drawbacks of this particular approach is unfortunately beyond the scope of this question, so please don't open this can of worms in the comments.)

In fact, once I had a journal submission returned to me because it was anonymous! The editorial assistant requested that I resend it with my name and other information proudly displayed. In that particular case, I had failed to follow the instructions. Don't make the same mistake I did -- follow the instructions!