You can use WinRAR (and probably other utilities) to see the list of files from the NITDroid-0.0.9.tar.bz2 package. You can also create a report using Tools -> Generate report (Alt+G).

Unfortunately, you have native directories (and also files) in your N900 with the same name on the bz2 package, so don't just go deleting stuff!

A quick comparison of my phone contents with the bz2 file shows that only the directories below can be safely removed:

• /cache
• /config
• /lost+found
• /mnt/asec
• /mnt/secure
• /mnt/secure/staging
• /mnt/secure/asec
• /mnt/sdcard
• /mnt/initfs
• /mnt/tmp
• /sdcard
• /system

It also shows that many commands that seems to be just links to /bin/busybox, and also /bin/busybox itself might have been overwritten. If you can still exec most commands in /bin (like /bin/ls, /bin/uname, /bin/df, etc.), then you're fine. Otherwise, tell me and we'll try to fix that as well.

(Or just backup as much data from your phone as you can and reflash it...)