I changed Octave's mechanisms around close() and closereq() functions to match Matlab's behavior.  See cset http://hg.savannah.gnu.org/hgweb/octave/rev/9213b8166af9.

@Pantxo: Interesting.  In the documentation I see

    The close operation executes the function defined by the figure CloseRequestFcn property. The default function is closereq.

    The closereq function unconditionally deletes the current figure, destroying the window. The closereq function takes advantage of the fact that the close command makes each figure specified as an argument the current figure before calling its respective close request function.

The closereq function honors the ShowHiddenHandles property setting during figure deletion and does not delete hidden figures.

So it is the case that closereq doesn't delete HiddenHandle figures, but if "clase all hidden" is used it must delete these figures too.  It sounds like 'close all hidden' changes the HandleVisibility property.

One other thing, could you test this in Matlab?

close all
figure
closereq

Does it issue a warning?

@Pantxo: Good work.  I checked in the patch here http://hg.savannah.gnu.org/hgweb/octave/rev/41cf6ee90cb6.

This is enough of a change that odd side effects are likely to crop up for a while.  For example, I tried this.

octave:2> h1 = figure
h1 =  1
octave:3> h2 = figure
h2 =  2
octave:4> set (h1, 'handlevisibility', 'off')
octave:5> close all   # At this point, h2 was closed
octave:6> close all hidden
warning: closereq: calling closereq from octave prompt is not supported, use 'close' instead
warning: called from
    closereq at line 38 column 5
    close at line 99 column 3

The problem is in closereq.m

  cf = gcbf ();
  if (isempty (cf))
    warning ("closereq: calling closereq from octave prompt is not supported, use 'close' instead");
    cf = get (0, "currentfigure");
  endif

The file closereq.m is trying to use gcbf to see whether a callback is executing.  It seems like either we could get rid of the warning (which still wouldn't work for hidden figures), we could modify close.m to reset the handlevisibility property of all objects that it is about to call the closerequestfcn, or we have to invent something in C++ graphics code that allows gcbf to show through for figures which are being deleted (maybe when the "beingdeleted" property is true?).

I looked through the m-files for gco, gcbo, gcbf instances which might cause problems.  The only ones that looked like they might be an issue were these from gcbf

gui/dialog.m:100:    "buttondownfcn", "if isempty (allchild (gcbf)), close (gcbf), endif",
plot/appearance/legend.m:1116:        && (isempty (gcbf ()) || strcmp (get (gcbf (), "beingdeleted"),"off"))
plot/appearance/legend.m:1136:      && (isempty (gcbf ()) || strcmp (get (gcbf (), "beingdeleted"), "off"))
plot/appearance/legend.m:1146:        && (isempty (gcbf ()) || strcmp (get (gcbf (), "beingdeleted"), "off"))
plot/draw/colorbar.m:262:      && (isempty (gcbf ()) || strcmp (get (gcbf (), "beingdeleted"), "off")))
plot/draw/colorbar.m:312:      && (isempty (gcbf ()) || strcmp (get (gcbf (), "beingdeleted"), "off")))
plot/draw/colorbar.m:335:      && (isempty (gcbf ()) || strcmp (get (gcbf (), "beingdeleted"), "off")))
plot/draw/colorbar.m:354:      && (isempty (gcbf ()) || strcmp (get (gcbf (), "beingdeleted"),"off")))
plot/draw/plotyy.m:207:      && (isempty (gcbf ()) || strcmp (get (gcbf (), "beingdeleted"), "off"))
plot/util/closereq.m:36:  cf = gcbf ();
plot/util/private/__add_default_menu__.m:89:    set (gcbf, "filename", fname);

I haven't reviewed any of the other instances besides closereq.m which I stumbled upon.

@Pantxo: The patch works very well for the issue at hand.  Looking at the documentation for the Figure "handlevisibility" property for Matlab

Visibility of figure object, specified as 'on', 'callback', or 'off'.

This property determines whether a figure is in its parent’s (the root’s) list of children. HandleVisibility is useful for preventing command-line users from accidentally drawing into, or deleting a figure that contains only user interface components (such as a dialog box).

If an object is not in its parent's list of children, functions that find objects by searching the object hierarchy or querying properties cannot return that object. Such functions include get, findobj, gca, gcf, gco, newplot, cla, clf, and close.

When the HandleVisibility property value is restricted using the 'callback' or 'off' settings, the object does not appear in the parent object Children property, figures do not appear in the root CurrentFigure property, objects do not appear in the root CallbackObject property or in the figure CurrentObject property, and axes do not appear in their parent CurrentAxes property.

In the third paragraph Octave now implements the first two conditions

1) object does not appear in parent object's "children" property
2) figures do not appear in root object's "CurrentFigure" property

Would it be possible for you to code a solution for the next two conditions as well?

3) object does not appear in root "CallbackObject" property (which gco() uses)
4) axes objects do not appear in their parent's "CurrentAxes" property.

As test code for the last condition,

hf = figure();
hax = gca;
get (hf, "currentaxes")
set (hax, "handlevisibility", "off");
get (hf, "currentaxes")

when I run that today I get

octave:40> hf = figure();
octave:41> hax = gca;
octave:42> get (hf, "currentaxes")
ans = -40.859
octave:43> set (hax, "handlevisibility", "off");
octave:44> get (hf, "currentaxes")
ans = -40.859

In Matlab R2016a:

>> close all hidden
h1 = figure (1);
get (0, 'children')
get (0, 'currentfigure')
set (h1, 'handlevisibility', 'off');
get (0, 'children')
get (0, 'currentfigure')
h2 = figure (2);
get (0, 'currentfigure')
figure (1)
get (0, 'currentfigure')

ans =

  Figure (1) with properties:

      Number: 1
        Name: ''
       Color: [0.9400 0.9400 0.9400]
    Position: [1256 1206 560 420]
       Units: 'pixels'

  Show all properties


ans =

  Figure (1) with properties:

      Number: 1
        Name: ''
       Color: [0.9400 0.9400 0.9400]
    Position: [1256 1206 560 420]
       Units: 'pixels'

  Show all properties


ans =

  0x0 empty GraphicsPlaceholder array.


ans =

  0x0 empty GraphicsPlaceholder array.


ans =

  Figure (2) with properties:

      Number: 2
        Name: ''
       Color: [0.9400 0.9400 0.9400]
    Position: [1256 1206 560 420]
       Units: 'pixels'

  Show all properties


ans =

  Figure (2) with properties:

      Number: 2
        Name: ''
       Color: [0.9400 0.9400 0.9400]
    Position: [1256 1206 560 420]
       Units: 'pixels'

  Show all properties

Confirmed.  Although the details are a little bit intricate and I have retitled this bug report to reflect that.

Octave does implement handlevisibility as shown below.

>> close all hidden
>> h1 = figure (1);
>> h2 = figure (2);
>> get (0, 'children')
ans =

   2
   1

>> set (1, 'handlevisibility', 'off')
>> get (0, 'children')
ans =  2

The problem is that while the figure is removed from the list of children, it is not necessarily removed from the "currentfigure" property.

I can get your example code to work by forcing the "currentfigure" property to be empty.

>> close all hidden
>> f = figure('handlevisibility','off');
>> set (0, 'currentfigure', [])
>> plot (1:10, 1:10)
>> findall (0, 'type', 'figure')
ans =

   2
   1