Public bug reported:

After five years of Unity, it is still possible to have discrepancies
between those three lists :

1. apps that are really open

2. apps that are marked as open in the dock

3. apps that are switchable from Alt+Tab

First bug : I just noticed that the Software Update app appears in (1)
and (2) but not in (3). This also means that it's not possible to switch
between its windows using Alt+backtick.

I report this as a bug in Unity instead of Software Update because I
believe that this is a more general problem that affects several apps. I
don't know Unity's APIs, but if apps are asked to report themselves so
that they appear in the dock and Alt+tab, and if it's easy to get it
wrong, then various apps will get it wrong, possibly even system ones
(see also my other bug report, which is about menubars). But if ever it
doesn't work that way and it's already fully centralised, then it's a
bug in Unity anyway.

I distinguish the lists (1) and (2) because it's possible that they be
different, and it could be considered as two other bugs if you will.
Those problems happen more systematically instead of seeming like random
mistakes in various apps' source code.

Second bug : it's possible and easy for an app to add one question-mark
dock icon per window. This seems to be the default behaviour in Tcl/Tk,
as the PureData app does this for every "patcher window" (document
window) that is open (it doesn't happen with properties windows (though
they're nonmodal) because they are marked as belonging to a specific
document, so that Alt+tabbing to that document brings a group of windows
at once.

Third bug : an app can have an icon associated to it but have the dock
unable to figure out that the matching app has been launched. For
example, if I launch PureData (/usr/bin/pd) from the dock or the app
search, the "Pd" icon shows up blinking and looks like PureData is
taking a long time to launch or has crashed during launch, but meanwhile
(and very quickly) PureData's main window pops up and appears in the
dock as a question mark. If I open PureData from a Terminal instead, I
get no PureData icon and only the question mark icon. This whole problem
could have a toolkit-specific solution (set the icon from the app
instead of from a launch item) but it could also have a global solution
involving an ability to get the name of the executable of the X11
connection that opened the app (obviously, it wouldn't work with remote
X11 apps, but those are rare, so it would be ok). It would have to check
for child processes, though, as PureData's gui is a child process of
/usr/bin/pd.

I also stumbled upon that bug when making a launch item for a specific
Windows app. When clicking on that app in the dock, the dock added a
WINE icon to itself instead, and failed to recognise that the icon I had
clicked on was for an app that had completed launching (it kept
blinking, and the triangle did not appear there, because it appeared
next to the WINE icon instead).

** Affects: unity (Ubuntu)
     Importance: Undecided
         Status: New

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https://bugs.launchpad.net/bugs/1673072

Title:
  Open apps (even basic system ones) can still be missing from Alt+Tab

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