* Hilighting all matches a selected word/part

Already possible with the "Mark all" keybinding and by double clicking on a word with the Addons plugin enabled.

Hilighting every exact match at message when doing "find document usage"

Should be possible but need to implemented by "someone".

* run external application

Not sure what exactly you mean but Geany can:

compile/build and execute the current file using Build commands
execute a configured custom command on the current word and pass this word as argument to the command, see Context Actions
send the selected to a configured command as input and replace the selection in Geany with the command's output, see Sending text through custom commands

* has % geany variable for the selected word/part

I don't understand this. Could you explain what exactly this means?

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