Your instruction files are addressing, not fragmentation
Merging every agent instruction file into a shared standard looks like deleting needless repetition, and for project setup it genuinely is. But most of what these documents hold is not a scattered copy of one thing; it is separate addresses, sorted by who a line applies to and who is allowed to write it. One of those boundaries is also a trust boundary, which is why the tidy fix of one universal file quietly hands repository text the authority of your own standing rules.