Another pop up to deal with? Can this be put behind a preference guard (interface.warn_on_replace_in_session in various)?

* Do people _really_ "accidentally" click the button, or is it intentional and they change their minds?  A new popup won't necessarily change the outcome of intentional actions.

Yes, happened for me twice. The last time it took me an hour or so to clean up my session again (I had to review each single file).

* The "in session" button is hidden by default, so new users don't see it on first use.

Geany remembers the fold state of the extra buttons and for me, they are always expanded because I need 'in document' and 'in selection' quite often.

* Popups like that just train people to click accept/press return twice/etc.

In some situations yes. Here it is rather a stopper in case you already realised you clicked the wrong button shortly after you clicked it.

* The change is saved in the undo buffer, so easy to back out.
  
  * Could undo be expanded so that the "in session" action can be undone, rather than the "replace all" in each file?
  * Or add a "reload all" command to reset to the last saved state.

Both variants only work if there are no othher unsaved changes in session files. Might not always be the case.

The main purpose of this confirmation is to make it harder to perform this heavy, very influential operation accidentally.
Other than 'in document' and 'in selection', 'in session' can be hard and time consuming to revert.

"In Selection" and "In Session" look very similar visually so they are easy to confuse.

Only when people are mindlessly clicking buttons. In that case, a popup isn't going to help.

See above.

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