Options passed to apps when opening from Dock vs Terminal command line

I have a much used freeware application called Aquamacs (it is a mac-specific version of the emacs text editor). If I open the application from the dock, I can not use it to "compile" .tex files written in the LaTeX markup language. However, if I start it from a terminal command line with no additional options:
/Applications/Aquamacs\ Emacs.app/Contents/MacOS/Aquamacs\ Emacs filename.tex
then everything works just fine. Evidently, beginning from the dock passes some additional option that interferes with LaTeX. Does anyone know how to control what options an application gets at startup from the dock? I would even be satisfied just to know what options are passed. Thanks.

From what I'm reading, you are working towards MDT but it's not approved yet, so the goal is to:
Deploy a "bundle" of applications as painlessly as possible without using UDI to make customizations quick.
Lets talk options then.
Option 1:  If machines types are in a unique OU or security group, create a collection for that and set these applications to mandatory install.  After initial deployment, the provisioner can drop the computer in the proper OU or group and you're
good to go.  Downside:  collections refresh plus client check-in makes this less than instant.
Option 2:  Orchestrator.  You can write a runbook that will approve and push apps.  You can then use the Orch console front end or a more friendly sharepoint/SM portal to push things out like a Manager would approve apps.  Downside:  if
not already deployed, there's no way they would approve that infrastructure if they are hesitant about MDT/UDI :)
Option 3:  PowerShell and WMI.  This should be doable ... but I've never tried it.  It looks like you're headed down the right path ... but i guess my question is:  if you can't have UDI when do get to pick the app?  Are you planning
to write a full multi-box for them to check their apps after the fact?  In that case ... just have the appcontroller URL pop up on first login ... might be easier than reinventing the wheel.

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