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This will be fixed in Textastic 3.0.
Implemented for Textastic 3.0:

If you quickly upload or download a file, there's a new "Always" button in addition to "Yes" and "No".

You can set this separately for upload and download.

You can re-enable the overwrite prompt in the settings screen.
There will be a whole range of themes available in Textastic 3.0.

Those are the same as in TextMate plus some additional ones like Railscasts, Monokai and Solarized themes.
In Textastic 3.0 you can bring up a list of recently used files by tapping on the name of the currently open file.

There's also a button to close the currently open file.

You can remove individual items from the list or clear the list.

This will be available in the next update.
I've implemented a new syntax highlighter for Textastic 3.0 that fixes the issue. It will be available in the next update.
I have implemented the symbol list from TextMate for Textastic 3.0.

Here's how this looks with an Objective-C file:

The debug log is generated by the libcurl library that is used by Textastic and I don't know a good way to prevent that. The passwords are only visible in the file for non-secure FTP connections. FTPS and SFTP connections don't leave the password in the log file.