irmin-pack: fix index integrity check for v3

[metanivek]

A few issues existed for running the index integrity check for v3 stores:

• Buffer for reading data never resized
• Dangling parent commits not able to decode length and considered "indexable"
• Store always used non-minimal indexing strategy

I've added more stores to our cram test so that we cover all of these issues.

Fixes #2264