Replicant

It appears to be crashing because of a missing resource. Are all the resources, xml and java files for an app still kept in an apk after installation or are they 'installed' to the standard directory hierarchy. If the former, could it be a corrupt apk that I could replace? Or reinstall replicant entirely? The only unique thing about my phone I can think of is that I removed both microphones internally for privacy (and front camera). I wasn't calling many people at the time of doing this, so I may not have noticed this causing the dialer to start crashing. I can't see the logical connection but perhaps there is some dependency.

EDIT: I have tried to test in safe mode but I cannot boot into it, I try holding both volume up and down on boot but I still have all non-system apps.

I have tried Dialer2 from fdroid and it crashes too, but looking at the log it seems to be for different reasons.
Below is from logcat over adb for the system dialer, all that was relevant to the crash (though I could be wrong):

11-11 10:04:36.061 6620 6620 E AndroidRuntime: FATAL EXCEPTION: main
11-11 10:04:36.061 6620 6620 E AndroidRuntime: Process: com.android.dialer, PID: 6620
11-11 10:04:36.061 6620 6620 E AndroidRuntime: Theme: themes:{}
11-11 10:04:36.061 6620 6620 E AndroidRuntime: android.content.res.Resources$NotFoundException: File res/drawable/ic_message_24dp.xml from drawable resource ID #0x7f0200d6
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at android.content.res.Resources.loadDrawableForCookie(Resources.java:2735)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at android.content.res.Resources.loadDrawable(Resources.java:2635)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at android.content.res.Resources.getDrawable(Resources.java:845)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at android.content.res.Resources.getDrawable(Resources.java:820)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at android.content.Context.getDrawable(Context.java:458)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at com.android.contacts.common.list.ContactListItemView.setDrawableResource(ContactListItemView.java:1527)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at com.android.dialer.list.DialerPhoneNumberListAdapter.assignShortcutToView(DialerPhoneNumberListAdapter.java:285)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at com.android.dialer.list.DialerPhoneNumberListAdapter.getView(DialerPhoneNumberListAdapter.java:138)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at android.widget.HeaderViewListAdapter.getView(HeaderViewListAdapter.java:220)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at android.widget.AbsListView.obtainView(AbsListView.java:2346)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at android.widget.ListView.makeAndAddView(ListView.java:1876)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at android.widget.ListView.fillDown(ListView.java:702)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at android.widget.ListView.fillFromTop(ListView.java:763)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at android.widget.ListView.layoutChildren(ListView.java:1671)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at com.android.contacts.common.list.AutoScrollListView.layoutChildren(AutoScrollListView.java:65)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at android.widget.AbsListView.onLayout(AbsListView.java:2148)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at com.android.contacts.common.list.PinnedHeaderListView.onLayout(PinnedHeaderListView.java:130)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at android.view.View.layout(View.java:16639)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at android.view.ViewGroup.layout(ViewGroup.java:5437)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at android.widget.FrameLayout.layoutChildren(FrameLayout.java:336)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at android.widget.FrameLayout.onLayout(FrameLayout.java:273)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at android.view.View.layout(View.java:16639)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at android.view.ViewGroup.layout(ViewGroup.java:5437)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at android.widget.LinearLayout.setChildFrame(LinearLayout.java:1735)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at android.widget.LinearLayout.layoutVertical(LinearLayout.java:1579)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at android.widget.LinearLayout.onLayout(LinearLayout.java:1488)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at android.view.View.layout(View.java:16639)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at android.view.ViewGroup.layout(ViewGroup.java:5437)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at android.widget.FrameLayout.layoutChildren(FrameLayout.java:336)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at android.widget.FrameLayout.onLayout(FrameLayout.java:273)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at android.view.View.layout(View.java:16639)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at android.view.ViewGroup.layout(ViewGroup.java:5437)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at android.widget.FrameLayout.layoutChildren(FrameLayout.java:336)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at android.widget.FrameLayout.onLayout(FrameLayout.java:273)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at android.view.View.layout(View.java:16639)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at android.view.ViewGroup.layout(ViewGroup.java:5437)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at android.widget.FrameLayout.layoutChildren(FrameLayout.java:336)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at android.widget.FrameLayout.onLayout(FrameLayout.java:273)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at android.view.View.layout(View.java:16639)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at android.view.ViewGroup.layout(ViewGroup.java:5437)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at android.widget.FrameLayout.layoutChildren(FrameLayout.java:336)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at android.widget.FrameLayout.onLayout(FrameLayout.java:273)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at android.view.View.layout(View.java:16639)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at android.view.ViewGroup.layout(ViewGroup.java:5437)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at com.android.internal.widget.ActionBarOverlayLayout.onLayout(ActionBarOverlayLayout.java:493)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at android.view.View.layout(View.java:16639)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at android.view.ViewGroup.layout(ViewGroup.java:5437)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at android.widget.FrameLayout.layoutChildren(FrameLayout.java:336)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at android.widget.FrameLayout.onLayout(FrameLayout.java:273)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at com.android.internal.policy.PhoneWindow$DecorView.onLayout(PhoneWindow.java:2934)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at android.view.View.layout(View.java:16639)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at android.view.ViewGroup.layout(ViewGroup.java:5437)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at android.view.ViewRootImpl.performLayout(ViewRootImpl.java:2179)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at android.view.ViewRootImpl.performTraversals(ViewRootImpl.java:1939)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at android.view.ViewRootImpl.doTraversal(ViewRootImpl.java:1115)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at android.view.ViewRootImpl$TraversalRunnable.run(ViewRootImpl.java:6023)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at android.view.Choreographer$CallbackRecord.run(Choreographer.java:858)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at android.view.Choreographer.doCallbacks(Choreographer.java:670)
11-11 10:04:36.061 6620 6620 E AndroidRuntime: at android.view.Choreographer.doFrame(Chore
11-11 10:04:36.064 2305 4566 W ActivityManager: Force finishing activity com.android.dialer/.DialtactsActivity
11-11 10:04:36.101 1930 1930 D gralloc : Registering a buffer in the process that created it. This may cause memory ordering problems.
11-11 10:04:36.102 1930 1930 E libEGL : called unimplemented OpenGL ES API
11-11 10:04:36.102 1930 1930 E SurfaceFlinger: glCheckFramebufferStatusOES error -1521756246
11-11 10:04:36.102 1930 1930 E SurfaceFlinger: got GL_FRAMEBUFFER_COMPLETE_OES error while taking screenshot