Maybe there are two things to add to your thoughts, Abraham:

Between 2. and 3. I would add (it's implied but I'd make it explicit):
2a. This new file in "edited" state does not have a proper file name and
not even a directory yet, it completely lives in a temporary folder.

One simple thing could be added to Frescobaldi's behaviour, and if I'm
not mistaken this is something Wilbert saw quite favourably on the
Github issue:
When a file or Frescobaldi is closed it is checked if it is saved, and
if not a dialog asks you how to proceed. At this closing time
Frescobaldi could also check if the current state of the file has been
compiled, and if not ask if it should do that before closing.

Personally I've never stumbled over this, but I can see that it may be
confusing or non-intuitive.

Urs

Am 22.10.2015 um 23:07 schrieb tisimst:
> Michael, et al,
>
> I think this thread has too many conflicting topics, and I'm
> definitely note sure what's causing some of the other issues that have
> been brought up (sorry!), but let's jump back to the OP's original
> issue as it relates to the GitHub thread you mentioned. If what I am
> about to say is NOT new, please feel free to ignore it, but hopefully
> this will help someone who is starting to use or is thinking about
> using Frescobaldi to create their LilyPond files.
>
> Here are some things I've learned about the Frescobaldi workflow (as
> they pertain to this topic):
>
>  1. All open input files exist in one of two states: "edited" and "saved"
>  2. Creating a new file starts the file in an "edited" state.
>  3. Opening an existing file starts the file in a "saved" state.
>  4. Any file that has been changed in any way is put in an "edited"
>     state. Even if you make a single change and "undo" it to the
>     original text, it is still considered "edited".
>  5. There are several compiling modes, but the most common are
>     "preview" (which enables point-and-click references in the PDF)
>     and "publish" (which disables point-and-click in the PDF). On
>     Windows and Linux, "preview" mode has the keyboard shortcut "Ctrl
>     + M" and "publish mode has the keyboard shortcut "Ctrl + Shift +
>     P". Not sure for Mac. These are VERY USEFUL.
>  6. Compiling the input file in the "edited" state creates a copy of
>     the input file (but no "included" files) and puts it in a
>     temporary folder. Any files that are output from this are thus
>     compiled to that temporary directory and NOT in the original input
>     file's directory. This temporary folder and its contents will
>     exist until Frescobaldi closes, then the directory and its
>     contents are erased.
>  7. Saving an input file does NOT save the PDF and/or MIDI files that
>     were previously compiled when the input file was in the "edited"
>     state. To update those, the input file (now in a "saved" state)
>     must be recompiled. The PDF and/or MIDI files will then be updated
>     and saved in the original input file's directory.
>  8. Compiling the input file in the "saved" state puts all output
>     files in the same directory as the input file, as expected.
>  9. You can force Frescobaldi to save the input file to its original
>     directory (and thus the PDF and/or MIDI files) every time you
>     compile by going to "Edit" > "Preferences" > "LilyPond
>     Preferences" > "Running LilyPond" and checking the box by "Save
>     document if possible". */NOTE: This does not apply to any
>     "included" files that are also open, whether in the "saved" or
>     "edited" state. It only applies to the input file being compiled./*
> 10. If any files are "included" in the input file (e.g., \include
>     "layout/choralSATB.ly"), LilyPond will always look for the "saved"
>     versions of these files. Thus, if any "included" files are being
>     referenced in "relative" mode (and thus not normally in LilyPond's
>     include path), then their directory must be added to LilyPond's
>     include path for "edited" input files to compile since the
>     temporary input file is placed in a totally different location on
>     the hard drive and the relative references are not valid there.
>
> You basically have to remember one thing: If you like the way the
> input file is, save it and re-compile (usually in the "publish" mode)
> one last time before you close up shop. That's it!
>
> Those are my thoughts. Maybe you knew all that already, maybe not.
> Maybe you just don't like that philosophy, which is fine. I totally
> respect that. I just think that if you could get used to working with
> these concepts, you'll find that they are pretty handy. I certainly
> have grown to like it because if I need to prototype something or I
> just want to try something out, I can do it without messing up a
> single file on my hard drive, knowing that anything I've made any
> potentially damaging changes to my saved files.
>
> Anyway, take that for what it's worth. I'm just trying to be helpful.
>
> Best,
> Abraham
>  
>
>
>
> On Thu, Oct 22, 2015 at 9:21 AM, Michael Hendry [via Lilypond]
> <[hidden email] </user/SendEmail.jtp?type=node&node=182557&i=0>> wrote:
>
>
>>     On 22 Oct 2015, at 02:02, tisimst <[hidden email]
>>     <http:///user/SendEmail.jtp?type=node&node=182547&i=0>> wrote:
>>
>>     BB,
>>
>>     I've been using Frescobaldi (Windows & Linux) for a long time now
>>     and I've never experienced what you describe (in terms of needing
>>     to close the file and reopening to get the output files I
>>     specify). What kind of computer/OS specs are you using?
>>
>>     - Abraham
>
>     I’m using Frescobaldi on an iMac.
>
>     I’ve just installed El Capitan, and I’m working my way through the
>     odd problems the new OS is throwing up, but I don’t think this
>     will change this problem as the developers of Frescobaldi agreed
>     that it exists (see the github
>     link https://github.com/wbsoft/frescobaldi/issues/646 ).
>
>     You should be able to demonstrate the problem on whatever OS you
>     use by following the steps I outlined in the linked conversation
>     above.
>
>     Michael
>
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