Yes, you will have to clear all these files.
The best way to install themes is by Eakrin's method. It checks and clears the existing theme and then applies the new theme, so you don't end up in a mess.
Flashing the phone and Master Clear will erase all the information in the phone, inclusing messages, contacts, calendar, files stored on your phone memory, i.e everything in phone.
For checking system files, you can install any app that enables you to view system files from your phone itself.
You can try from the below:
yan0's My Stuff - Here
XPTools - Here
MFile - Here
To View the system files on PC, you can telnet it but I don't know if you'll be able to make changes.
You can also use RadioComm but it is a complex process.



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