1998 Civic EX (D16Y8) manual transmission.

Intermittent squeaking noise that seems to be coming from manual transmission.
All belts are less than 6 months old and sound is not coming from front of the engine. The squeaking noise is present at idle in neutral or whether the clutch is engaged or disengaged. Not noticeable when driving, but may be masked by usual engine and road noise. Car runs fine otherwise and no grinding or knocking noises either. Is this normal noise for a 6th gen civic or should I be concerned? I'll post a video with the squeaking noise later today if need be.

 

could be a throw out bearing

 

A video may help.

Have you ruled out a loose drive belt (power steering, A/C, alternator) or a squeaking pulley (alternator, idler, compressor, power steering) on the left side of the engine?

Have you checked for a loose or cracked exhaust heat shield?

A bad throw out/release bearing would only squeak when the clutch pedal is depressed.

 

Belts are tensioned correctly. Could be a pulley, but the noise seems to be coming from the back of the engine/transmission area. Would using WD40 to lube pulleys work temporarily to rule them out as possible issue(s)?

Not currently using an exhaust heat shield.