BF2Modtools.exe is, as you know, the developer executable version of the game. You can access a pseudo-command line in the tools by pressing the "`" button (this is the button to the upper left of your keyboard, just next to "1" and under "Esc").
There is a long list of things you can do using this particular interface. If you press "Tab," you can scroll through a list of command prefixes (like ai., combo., render., etc.). If you press enter on just a prefix, you can see a list of suffixes that you can use with that prefix to create a full command.
For example, you can see how I used the command "EntityProp.Enable" (which toggles prop meshes, but not collision meshes, on and off) to make normal Mos Eisley:
Some of the commands in here, you will notice, require you to run a command line parameter before opening the modtools. For example, combo. commands will ask you to set "/debugcombos" on the command line to use them, like this:
You can either run your modtools through the command prompt, or you can use a batch file like this one:
"BF2ModToolsDEBUG.bat Download
That batch file can be used by placing it in your "GameData" folder (with BF2Modtools.exe) and running it instead of the modtools.exe. It enables the combo debug commands and the animation debug commands, two of the more useful ones I saw. Any additional debug commands can be enabled by opening up the batch file and editing it as common sense would dictate.
So, for example, now that you have combo debug commands open, you can use it to show the damage area of combos, like this (note that the red wireframe spheres represent area in which damage is being done;):
Note that this uses the command "combo.Damage". At any time you may exit out of the debug interface by pressing the "`" key again.
(You may notice in the last picture I removed the green bar; this is not recommended as it will remove the interface (menus etc.) entirely.)