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I use the file extension php5. When running the automatic update from RC7 to RC8 it required me to have the extension .php before it would confirm the files were updated.

I've listed the steps below to try and explain it better.
1) Download the changed files rename all .php to .php5, upload
2) Check files again
3) All non .php files were confirmed as being updated
4) Download the changed files and upload
5) Check files again
6) Processed finshed okay
7) Manually delete .php files

I understand the problem. Currently, the update information itself is having hardcoded extensions listed - therefore only comparing files with the extension .php.