What you (probably) want is called 'condensing the changes'.
Have a look at the class PharoChangesCondenser.

<< I create a new more compact changes files with a single version of each method in the image. >>

> On 06 Jul 2015, at 11:08, Peter Uhn��k <i.uhnak@gmail.com> wrote:
>
> Is it possible to remove all references to a class after it has been removed everywhere?
>
> For example I can delete all classes of package 'Roassal2-Builder-Grapher'
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> pkg := RPackageOrganizer default packageNamed: 'Roassal2'.
> grapherTag := pkg classTags detect: [ :each | each name = #'Builder-Grapher' ].
> grapherTag classes do: [ :each | removeClass value: each ].
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
> However this leaves the .changes file intact, even after I do "Smalltalk cleanUp: true".
>
> The reason why I am doing this is to lower the size of .changes/.images files which are massive just after loading my project... so it takes a lot of space for testing...
>
> Thanks,
> Peter