MakeMDL is the primary compiler for objects created for Microsoft's Flight Simulator 9
In its latest iteration, available in the MakeMDL SDK  for FS9, it supports input commands via a file named "makemdl.cfg".
Normally, this file is located in the same folder in which MakeMDL.exe resides, e.g. "C:\gmax\gamepacks\fs2004\plugins"
Makemdl.cfg options explained
Of special interest to avid modellers for FS9 are the "Debug", "KeepErrorLog", "WeldPoints", "Optimize" and "Flatten" settings.
- Set to "1" (no quote marks) to enable debug functionality
- Automatically opens the log file after compilation if set to "1"
- Does not delete the log file if set to "1"; useful for finding erroneous parts or animations
- Does not delete temporary files created during compilation if set to "1"
The next three settings can be a cure to the 4mm vertex weld issue otherwise present for FS9 models (very notable and annoying in virtual cockpits)!
- Disable vertex welding when set to "0".
- Optimizes code (grouping of parts with same materials and removing unnecessary translate/rotate animation tags)
- Set to "0" to disable flattening of the hierarchy tree
- Does not parse animations during compilation if set to "1"
- Set to "1" to enable reflectivity for the model. Make sure to put a "_t" suffix into the texture's file name, e.g. "fuselage_t.bmp" and make sure "Reflections" is enabled in FS9's "display" menu.
- Enables use of auto-enabled night textures ("_lm" suffix, i.e. "tower_lm.bmp") if set to "1". You won't need to fill the "self-illumination" slot of the material in GMax. Useful for scenery design!
- Enables use of self-illumination night textures ("_l" suffix, i.e. "fuselage_l.bmp") if set to "1". You won't need to fill the "self-illumination" slot of the material in GMax. Useful for aircraft design!
- Enables damage textures if set to "1". Not needed for FS9.
- If your object appears upside down in FS9, set this to "1".
- Set this to "1" to invert the left/right coordinate axis
- When set to "1", the bank and heading axis of the model will be swapped
- Set to "1" to enable crash detection when compiling a scenery object.
- Produces a sample placement XML file for a scenery object when set to "1"