The trans, pedals,
cabling, interior panel replacements,
shift lever
assembly, modifications or replacement of the wiring harness (A dealer probably won't modify the harness), a new ECM with calibrations... can possibly impact other modules due to how cars are these days.
Pressure plate
assembly, clutch release bearing, release bearing retainer,
shift cable / detent
cable, linkage, transmission computer, clutch master cylinder, clutch slave, cylinder,
shifter assembly /
shift knob, transmission cooler and cooler lines.