The list of Projects and their coordinate transform types can be saved in a special file called the "Merge Description File" with file extension .pmm. This file is an ASCII file that you can view in a text editor if you wish.
You save your current merge list by pressing the "Save..." button in the Merge Description File area. A file dialog will appear allowing you to name the file.
You can then load that description at a later time.
A common approach to handling a large project would be to work on the sub-projects and then execute the merge only to see or export the file result. You may then be executing the merge quite often as you go back to change items in the sub projects. The Merge Description File makes this easier.
The easiest way to create a Merge Description File is to open PhotoModeler, set up a known merge of projects, then save a Merge File (click Save button on the dialog) and use it as a template for the syntax. The following shows examples of the contents of a Merge Description File:
No transform:
"E:\Projects\Project 1\p1.pmr" 0
"E:\Projects\Project 2\p2.pmr" 0
With a Named Point and Coded Target Match transform:
"E:\Projects\Project 1\p1" 0
"E:\Projects\Project 2\p2" 1
With a Translate transform:
"E:\Projects\Project 1\p1" 0
"E:\Projects\Project 2\p2" 2 10.000000 10.000000 10.000000
Three projects with a Named Point and Coded Target Match transform:
"E:\Projects\Project 1\p1" 0
"E:\Projects\Project 2\p2" 1
"E:\Projects\Project 3\p3" 1