Samtools cat naively copies all incoming containers, and then writes
an empty EOF container when closing the file.  This leads to multiple
internal EOF markers as they're implemented in CRAM as an empty
container.

Oddly there was code explicitly dealing with this, which seems
redundant.  Perhaps it served a purpose in early versions.  Regardless
internal EOF markers is permitted and are ignored, so this change is
just for tidyness sake and to improve robustness incase bad
implementations stop on the first EOF.

Amend previous commit following review comments.  (As a distinct
commit temporarily so the change we discussed is visible.)

Empty containers still have a CRAM compression header block.  So EOF
blocks internal to a file need to have their block read even if we're
not going to write it and the container back out again.

This was visible by the following experiment.

// Create a CRAM with internal EOF markers
samtools-1.12 cat in.bam in.bam -o out1.bam

// Concatenate such files together, with code prior to this commit
samtools-previous-commit cat out1.bam out1.bam -o out2.bam