I did the following:
extract some sources from a zip file so that they are
on the filesystem in e.g. d:/work/math/...
Then create an IDEA project around it, with srcdir=d:/work
ok, then the package structure did not match filesystem.
correct is e.g. abc/def/someothermiddlepackage/math/...
so I did create package from IDEA (which is convenient when
you write abc.def.someother..., to create multiple packages at once).
Then I move the source files from math to abc/def/...
so that they are in the correct place.
So far so good, IDEA notices the changes.
Then I delete a few source files from IDEA (alt-f1,
show in project view, delete).
And one file just refuses to get deleted!
The editor gets closed, it disappears from project view,
but it stays on filesystem!!!!