This is on a clean install of stock Fiji, ImageJ 2.0.0-rc-65/1.51s,
downloaded today (2/2/18).
First run Help>Update ImageJ… This upgrades Fiji to
ImageJ 2.0.0-rc-65/1.51t. Now run Help>Update… The updater
runs the update check and then pops up a warning box, “Warning”
“There are locally modified files!”. (The proposed changes window
is empty, probably because there are not yet any updates for the
freshly downloaded Fiji.)
I also ran this test with a clean install of an older Fiji download
(ImageJ 2.0.0-rc-62/1.51s, downloaded 12/27/17). Running
Help>Update… upgrades Fiji to ImageJ 2.0.0-rc-62/1.51t. Then
running Help>Update… gives the same “There are locally modified
files!” warning. For this older version of Fiji there are several proposed
changes in the Updater window. If I carry on (first click “OK” on the
Warning pop-up) and click “Apply Changes”, a “Resolve
dependencies” window opens up with the choices:
Keep the local version
If I select “Keep the local version” the update appears to run
correctly, and when I quit and restart Fiji, it reports as its version
ImageJ 2.0.0-rc-65/1.51t. Note, this version ID suggests that both
updates are in effect, as both rc-62 --> rc-65 and 1.51s --> 1.51t.
(I don’t see anything that suggests that Fiji is messed up, but I don’t
have any good way to check.)
At a minimum, the “There are locally modified files!” warning is a
worrisome (semi-) false alarm. Or perhaps it indicates that the
doubly-updated Fiji installation is subtly broken somehow.
What is the approved approach to keeping a Fiji installation updated?
Should one not run Help>Update ImageJ…? Should one run
Help>Update ImageJ…, and ignore the “There are locally modified
files!” warning, and select “Keep the local version” when Fiji
auto-updates (or when running Help>Update…)? Should one
not run Help>Update (and not permit Fiji to auto-update)?
A word or two about what the two separate updates are for would
be appreciated, as well.