In the context of a larger discussion where most requirements are already understood, all of the possibilities you mention ‒ ie,
• We just need minified and concatenated files
• We need just minified and concatenated files
• We need minified and concatenated files only
‒ probably will be understood to mean the same thing:
• Of the proffered file characteristics, we need minified and concatenated and don't need any others, and we still need other capabilities that were previously and separately stated.
However, if a larger context hasn't been given, those three forms can have slightly different interpretations, as follows:
• We just need the files that have been minified and concatenated and we don't need any other files.
• We need just the characteristics or capabilities of minifying and concatenating files, without excluding other previous and separate capabilities.
• We need capabilities of minifying and concatenating files, only; we don't need any other features or capabilities.
That is, the first form may be thought to address necessary files, the second to address required file characteristics or capabilities, and the third to exclude not-mentioned features or capabilities. Note: The reasonable thing to do is use a few more words or sentences to make your meaning clear.