[FIRRTL] Add layers output file to file list

[SpriteOvO]

Fixes #7542. @FanShupei Could you try if this PR fixes the issue?

[seldridge]

I thought about making this change, too. I went another direction with ChiselSim, though, which was to have it look for files that are layer enable files and include the ones that enable the layers the user wants.

I.e., the filelist today can be used to compile the design without any layers enabled. This would change this to mean the filelist will compile the design with all layers enabled. If we keep the filelist, it seems like we just have to choose one of these.

How were you thinking of using this?

[sequencer]

I personally like the idea of removing the entire filelist.f. because of the lack of consistent ABI for it. random user will get trap because of issue like this. Maybe a new API to query MLIR might be possible?
e.g. query all public module, query different layers, query memory metadatas.