I've released masontidy 2.53 which tidies <%perl> blocks and %-lines together. 
It should also handle the case below with intervening methods, btw.

 Give it a try and let me know how it does on your code base.

Jon

> 
> I think basically all the perl sections should combine with all the inline 
> sections but I can't imagine how you will do that.  I do NOT think it would 
> be necessary to support weird constructs like main component perl sections 
> that have other sections embedded in them.  For example
> 
> 
> <%perl>
> some perl code
> </%perl>
> some HTML
> other HTML
> % inline mason
> 
> <%method something>
> <%perl>
> 
> .....
> </%perl>
> embedded HTML in a method
> % inline in a method
> more HTML
> <%perl>
> another block 
> </%perl>
> 
> </%method> 
> 
> % other inline mason back in main component
> <%perl>
> perl in main component
> </%perl>
> some embedded HTML in main component
> 
> I probably do nonsense like that, but if I do I should really be moving those 
> methods to the end of the component.
> 
> 
> 
>> When running masontidy on a sample file I get a lot of output like "Ignoring 
>> -b; you may not specify a destination stream and -b together".  Not sure 
>> what that means, but I assume it is something from perltidy.
> 
> No idea, did you put -b in your perltidy options list? You shouldn't need to.
> 
> I am an idiot - I forgot there even WAS a local .perltidyrc.  I haven't used 
> perl tidy on that project in years.  Thanks!
>  
>> When building on a Windows machine the generated .bat file works fine, but 
>> the generated native perl has the wrong #! line in it.  Not sure if there is 
>> a way to fix that, but if there is then it would work right when called from 
>> a Cygwin shell on Windows (I use that for a development environment 
>> sometimes).
> 
> I just have #!/usr/bin/perl at the top of bin/mason, I've always thought that 
> was the correct thing to put. I don't have a Windows environment but let me 
> know if you figure out a way to fix it.
> 
> I will give it a think.
>  
> -- 
> Shane McCarron
> halindr...@gmail.com

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