I want to create a movie with H.264 video and HE-AACv2 audio. Since ffmpeg/faac doesn't support HE-AACv2 (as far as I know) I would use neroAacEnc to create it. Is there any way to do that in Kdenlive render profile? Or to add arbitrary shell commands to it, so I could render the movie with PCM audio, then split the audio track out, re-encode it with nero and reassemble the mp4 file.

Basically, no, you can not use an external program. You can render audio only to WAV, transcode it with Nera, and then mux it into the MP4. However, you do run the risk of losing audio synchronization going through these steps - plenty of room for problems to creep in. aacPlus2 really only makes sense when you need 48 kb/s or less like for mobile streaming. Do you really need that?

Actually I use the 48kb/sec HE-AACv2 for music and movies on my Nokia, yes. :) File size for "near CD quality" is about 30% smaller than LC-AAC (and 80% smaller than high-bitrate MP3). I already have scripts to convert the audio track and re-mux like you described, I was simply curious if a post-render script or encoder plug-in or anything like that could be used in a render profile for my phone. It's not a big deal and I can continue to run the script manually until someday when (or if) HE-AACv2 is supported by the common Linux multimedia programs. Thanks!

In the render profile, you can add a post="command options etc", which MLT understands, but Kdenlive has no way to insert your output file name into there.