If we already have the file file in the Tree data base it means it was loaded already from content data file.
The only files we need to hanlde are the new files which were moved\copied from other location (which exists in the content data file)

My openion:
The unless is above since this is the common case (the manual flag will be used rarly). 
In terms of performence, the jump prediction of if else clauses takes the first block as the true prediction.
I think that the comment MANUAL MODE  is good to understand the block. 
What do you think?