Noticed the same problem (uncomment commentary lines) in
filetype_extensions.conf geany.css snippets.conf ...
Oh boy, this looks like a pervasive issue.
If I go to "Tools --> Configuration Files --> Filetype Configuration", and choose anything in there, the file that comes up seems to have this same problem: lots of lines that are just prose/commentary, but they're not commented. (Not sure what this means, but in the window title bar they say paths like ~/.config/geany/filedefs/filetypes.whatev, but in that directory I only see filetypes.common and filetypes.README.
Tools->Configuration Files-> etc toggles comments when it opens the file for the first time, which should add #~ to every line. Have you changed the toggle comment setting for .conf filetypes?
In "Preferences --> Editor side tab --> Features tab", the "Comment toggle marker" is blank / empty. Maybe at some point I removed the tilde there because I didn't like how it looked... (? can't recall. Ah, I think at one point I put a single space in there).
I wouldn't know how to change the toggle comment setting for a particular filetype --- I only know the prefs setting I just described above.
Ok. Thanks, I put the "~" back into that "comment toggle marker" field.
The reason this is done is because the edited file is saved in the users config, and overrides the system file. If all settings were set in the user file any fixes in a new version of Geany would be overridden by the old user settings. So they are all commented out (using toggle comment) and the user can just toggle comment for the section titles and settings that they need to change, leaving the rest to be the system values.
Gotcha. Thanks for the explanation.
-- John