some additional surgery was needed to get the checksum value out

- wrong number of reps causes cppsim bugs and reading from empty stream
- adjusted cppsim I/O wrappers to reflect changes in HLSCustomOp

[Docker] Add specific version for markupsafe (python package that gets usually installed when installing jupyter)

This reverts commit b419957e.

this commit moves all git repo-based dep cloning to ouside Docker,
and their installation commands to the entrypoint script

Support for optimized 1D dws SWU