Update ILRepack to not rely on ordering

ILRepack currently relies on the ordering of the input assemblies to find the "main" assembly. This is rather fragile and leads to issues like #1426. Make this more robust if possible.

Locate the ILRepack invocation and the logic that chooses the main assembly, then review issue #1426 for the ordering-related failure. The work is done when main-assembly selection no longer depends on input assembly order and the reported issue is addressed.

Written by the indexing model from the issue text.