What do you think about having a "Duplicate this alias file" button or feature (1) in the program, similar to the existing "Make a duplicate copy of this entry" under Aliases/Groups? If it is a read-only alias file, maybe it gives the option of disabling the existing alias file (2), and automatically create the new alias file in the MyCustom folder.
For this to show the proper icons (without having to copy them), I would further suggest a common icon path (3) that can be used by all aliases (with /ICON) regardless of the alias location.
This is nothing can't be done already using the file system, but makes a little easier I believe. The helpfile seems to be out of date (4) as well:
- These .alias files are located in the AliasGroups\ subdirectory of FARR, and are further broken up into AliasGroups\Installed and AliasGroups\MyCustom
Since I didn't see that folder, I initially created it and when that didn't work, I looked in the %appdata% folder. After doing a search of my system, I found the MyCustom folder in My Documents.