Recording and editing any serious session might leave the session with some unused or misplaced files here and there. Ardour can help deal with this clutter thanks to the tools located in the Session > Clean-up menu.
When importing media files, if the Copy files to session hasn't been checked, Ardour uses the source file from its original destination, which can help avoiding file duplication. Nevertheless, when the session needs to be archived or transfered to another computer, moving the session folder won't move those external files as they are not in the folder, as seen in Backup and sharing of sessions.
Using the Bring all media into session folder menu ensures that all media files used in the session are located inside the session's folder, hence avoiding any missing files when copied.
Ardour represents audio waveforms with peak files, that are graphical images generated from the sound files. This generation can be time and CPU consuming, so it uses a cache of the generated images to speed up the display process. To watch for files modification, Ardour relies on the file-modification time. If an external file is embedded in the session and that file changes, but the system-clock is skewed or it is stored on an external USB disk (VFAT), Ardour can't know the change happend, and will still use its deprecated peak files.
Using the Reset Peak Files menu allows to reset this cache, which frees up disk space, and forces the re-creation of the peak files used in the session. It can prove useful if some waveforms are not used anymore, or if a graphical or time glitch happens.
Recording usually lefts a lot of unused takes behind, be it in midi or audio form, that can clutter the Region List, and eat up a lot of hard drive space. While its generally a good practice to keep as many things as possible while recording, when transferring or archiving the session, some clean up can help a lot in reducing the sessions clutter and size.
Selecting Clean-up Unused Sources… will force Ardour to detect those unused waveforms by looking for unused regions, and (through a prompt) for unused playlists. The media files won't be destroyed, though. At this stage, they are just copied in a particular place of the session path (namely, in the dead sounds/ sub-folder).
Although Ardour is a non-destructive audio-editor, it allows for a very careful destruction of unused media materials. This function is closely linked to the previous one. When the unused sources have been cleaned up and quarantined, the Flush Wastebasket menu will allow for their physical destruction.
As a safeguarding mechanism though, Flushing the wastebasket in impossible in the same working session as the Cleaning up of unused sources: the user needs to close the session and reload it before flushing. It allows to test the playback of the session and ensure both that Ardour didn't commit any mistake (unlikely, but better safe than sorry), and that the user is absolutely sure of what he does.
Notice that all media destroyed this way is not sent to the system's trash can but permanently deleted. If a file is mistakenly destroyed this way, the user will have to rely on data recovery techniques to try getting it back.