I'll try to address all your questions below. Our IDE indeed only allows one target per project. While this configuration probably won't ever change, we do plan on allowing multiple projects open within the same instance of Simply Fortran. Multiple projects is planned for version 3.
You should be able to add non-existent files via the "Add File(s)..." option in the Project menu. After you navigate to the directory, you can just type in the name of the file and click Ok. It doesn't have to exist, and it also isn't actually created until you open it in Simply Fortran (from the Project Outline), edit it, and save it. It's not ideal, but Windows allows it.
I do like the idea of highlighting TODO statements in comments. I'll see what can be done.
Unindenting end statements has been problematic in the past. It probably won't ever work in fixed-format Fortran. However, it does work in free-format Fortran (Fortran 90 and higher, generally) if you enable Syntactical Indentation in the Editor Settings window under the "Language Features" tab.
The abstract keyword should absolutely be highlighted.
I'll examine what's possible as far as pretty-printing the project files. I'm not exactly sure what the library we're using supports. It would make source control much nicer.
The makefile issue is more complicated. Simply Fortran uses Open Watcom Make, or wmake, as opposed to GNU Make. The decision to use wmake is as old as Simply Fortran, and it's based on plenty of issues encountered with GNU Make under Windows. If you examine the Makefiles generated by Simply Fortran, you'll notice it uses an Open Watcom directive, ".SYMBOLIC," as an example of it not being a GNU Make makefile.
Additionally, Simply Fortran uses makefiles out of convenience rather than providing portability. Make systems are quite good at handling dependencies. The files generated, though, were never meant to be used outside of Simply Fortran, honestly. The hard-coding of compiler paths in the makefile is because only Simply Fortran itself is expected to use the makefiles.
I do understand what you're suggesting, though, so I will look into handling them differently. The hard-coding is ugly, but it developed as a working solution to a messy problem on Windows.
I'll look into eliminating links for the runtime functions in profile results.
Promoting Simply Fortran as working under WINE will be a moot point soon. We're currently testing a Linux native version that should be shipped before the year's end. We're trying to fix up some packaging issues that we're finding, but the application looks great.
The GNU/Linux version I mentioned above is a true GTK+ 3 application. Simply Fortran for Windows is a normal Win32 application, written mostly in C and using the Windows API. Because it uses this long-supported API, Simply Fortran actually works fine on Windows 2000 and Windows 10. We don't promote Windows 2000 compatibility, though.
Thank you for all the questions, though! I'll start looking into your suggestions next week.
Jeff Armstrong
Approximatrix, LLC