DOCS - write up the type of files used by Proteome Discover 2.2 (PD2.2)

## Description
- PD2.2 has several proprietary files that are not very well documented.
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- [ ] Make list in this thread of all of the files present:
    - [ ] before search
        - `.raw`
        - `.tune`
    - [ ] during
        - `.scratch`
        - `.pdstudy`
    - [ ] after
        - `.txt`
- [ ] Retrieve whatever info possible on these files from the PD2.2 User Manual.