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iPad apps are sandboxed. Files in an app stay inside the app unless you export/share them to another app (which just creates a copy of the file inside that other app). iOS doesn't have a user accessible file system like Android or Windows. Calibre Companion is actually unnecessary but can be useful depending on your requirements. I read epub files and I use Marvin. I just use its built-in Dropbox support to transfer files from my PC to Marvin.
Honestly, better to find an app that fits the "reading" portion of your requirements first and then just figure out the best method to transfer files to it later.
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