I agree with John. Most likely a "compile on save" / "files watching" problem 
than something Git related.

--emi

‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐

On 10 March 2018 8:12 PM, John Muczynski <johnst...@gmail.com> wrote:

> Hi Owen,
> 
> I see Brett is posting about the git portion of your questions.  I'll try to 
> answer some of the others.
> 
> >I observe some compilation errors.
> 
> > Is something being cached
> 
> I also get this symptom when making changes to a large number of files in a 
> project.  I think the root of the issue may be the file watching. When lots 
> of files get changed, the buffers get flooded. For me, this is the buffers in 
> the operating system (windows !@#$%&).  The result is that NetBeans doesn't 
> immediately recognize some of the changed files. It does seem to go through a 
> slow polling loop and eventually recognize all the changes, but then the 
> symptoms here branch into two categories.
> 
> 1\. the red marks for compile errors go away on their own, or you hurry it 
> along by opening one of the classes or doing a rebuild or whatever.
> 
> 2\. the red marks stay no matter what you do.
> 
> 1\. In the first case, I don't think there's much to be done about it other 
> than a significant rewrite. The symptoms here may accidentally change with 
> JDK 9, so I look forward to using NetBeans 9 with JDK 9 at some point. Part 
> of this story is that classes seem to be getting compiled twice: once into 
> class files on disk and a second time into RAM. Notice, for example, that if 
> you do a clean and then a build that it doesn't speed things up.
> 
> 2\. In the second case, I do see sticky red marks that don't go away.  
> Deleting the NetBeans cache does fix that. I've found it more helpful to 
> delete the cache when NetBeans isn't executing. I seem to remember seeing 
> people making a plugin for NetBeans for deleting the cache.
> 
> Kind Regards,
> 
> Johnny
> 
> --
> 
> Johnny Muczynski
> 
> 734-262-2045
> 
> On Sat, Mar 10, 2018 at 5:10 AM Owen Thomas <owen.paul.tho...@gmail.com\> 
> wrote:
> 
> > Hello.
> > 
> > I have been using NetBeans with Git (I moved my codebase from SVN about 
> > about ten months ago), and I seem to have some problems after I open a 
> > clean working copy.
> > 
> > After I commit my changes, I sometimes observe that some blue cylinder 
> > embellishments remain next to some packages. I backup my .git file, delete 
> > the original, and restore it from backup. Sometimes, after checking out a 
> > working copy and after reloading projects into NetBeans, I observe some 
> > compilation errors. It seems that there are also some uncommitted changes, 
> > and removing these changes seems to remove the compilation errors.
> > 
> > Has anyone got a clue as to what might be going on? Is something being 
> > cached in NetBeans somewhere?
> > 
> > Thanks,
> > 
> >   Owen.

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