I do sometimes wish Geany could remember markers when it closes.
I don't know if this would work or not, but what about adding some extra info
to '.geany' files?
I don't know a lot about the file format, but under the [files] section, a
typical file line might look like:
FILE_NAME_0=0;C;0;EUTF-8;1;1;0;%2path%2Fto%2Ffile.c;0;4
Could there be a section for markers as well?
FILE_NAME_0=0;C;0;EUTF-8;1;1;0;%2path%2Fto%2Ffile.c;0;4;M55M117M476M1002
Where the line numbers are separated by 'M', so this would mean that there are
markers at lines:
55
117
476
1002
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