Well a "Factory Reset", is different than a "Hard Reset". The former will allow for leaving some files, or trying to. The latter will not.
Misc. files can be a multitude of things created by you, apps, the OS, etc. The only way to start truly fresh would be to save all your personal data and files (not apps) to a could account, google account or other device (computer, etc.) and then do a "Hard Reset". This will wipe everything from the device and start it back up as it originally was. Then you can add and remove apps and files as you wish. Just be sure to look at the used stuff and storage prior to adding anything.
NOTE: Doing this will clear 'all' the data on your phone, so it is suggested you not choose this option unless you have to, or aren't worried about losing anything on the phone.
Be sure you back up any data you want to keep, to a computer or cloud account, before doing the reset.
To "Hard Reset" the phone...
1. Make sure that the phone is actually powered off.
2. Remove your SD card, if there is one in the device.
3. Press the "Power" and the "Volume Up" buttons, together, until you see the start-up logo on the screen.
4. Once you can see the logo, release the buttons and allow the device to enter the "System Recovery Mode".
5. Next use "Volume Down" button to get to the "wipe data/factory reset" option When in recovery mode the "Volume Up" and "Volume Down" buttons are how to can navigate and highlight what option you need.
6. Once you have selected the "wipe data/factory reset", press the "Power" button to select that option.
7. On the following screen, repeatedly press the "Volume Down" button until the "Yes - delete all user data" option is what is selected.
8. Then press the "Power" button to hard reset the phone.
9. If you took your SD card out in step 2, when the device is up and running again, reinsert the SD card.
Doubtful. Some you may wind up with removed if you remove certain apps, or if the app isn't removable then clear its data, force stop the app and then disable it. All of which can be done in "Settings" then "Apps" and then choose the "All" list.
But be careful with which apps you try to do this. Choose the wrong one and you can seriously mess up the device.