The pull request that I submitted has been reviewed once by one of the Galaxy core developers, John Chilton. Our brief conversation can be seen below:
As you can see from my comment, the fix was updated the same day. Below you can see diffs of the 2 files that were changed (and then updated).
Effectively, the versioning in the XML is so that when the next Galaxy update is rolled out there will be no compatibility issues. This is because in Galaxy a user can create workflows. These workflows are merely culminations of tools that feed input and output to each other in order to produce a final end result (or results). If someone updates their Galaxy, they will essentially be notified that their workflow will not work anymore unless they tweak the X tools that have changed versions.
The filename change is something I almost did initially. Galaxy preserves files in working directories. When a job (the running of a tool - analogous to a process and program) runs it can have files created that only need to exist during the duration of the job. By naming the file irrelative to the name of the inputfile that it is initially handed, Galaxy can tag this and pretty much say "Alright, when we're done, this is getting thrown away". We just do not want people to have clutter on machines running these tools.
So next up for Team Rocket is finding a new bug to squash, find documentation that needs to be updated/fixed, and/or find a feature request and create that feature. Personally, I would much rather go with the bug or feature as that is actually fun versus reading someone else's documentation and testing everything to make sure it works. Killing bugs and adding features actually adds more usability, especially since documentation appears alongside new/fixed code.
Music listened to while blogging: Tech N9ne
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