Here is an excerpt from the file listing under backup-dir/datadir/mem for a backup from a MySQL Enterprise Monitor repository database. Notice how the .ibd files for InnoDB tables are now compressed to .ibz files, while other kinds of files are left unchanged.

inventory_types.frm
inventory_types.ibz
log_db_actions#P#p0.ibz
log_db_actions#P#p1.ibz
log_db_actions#P#p2.ibz
log_db_actions#P#p3.ibz
log_db_actions#P#p4.ibz
log_db_actions#P#p5.ibz
log_db_actions#P#p6.ibz
log_db_actions#P#p7.ibz
log_db_actions#P#p8.ibz
log_db_actions.frm
log_db_actions.par
loghistogram_data.frm
loghistogram_data.ibz