[Sync-En] yar: fix unresolved exception entity references

[lacatoire]

Sync with EN commit 28975cb447c4d3e13fdfd2f9c1eb3e8b7c231e3f (php/doc-en#5778).

• Reference the seven exception classes from book.xml, they were never included
• Replace the self-referencing &Methods; block with an &InheritedMethods; include of class.exception on each exception page
• Remove the undefined &reference.yar.entities.*; entities
• Delete reference.xml, an orphaned file included by nothing

Fixes: #1066