Fix recalculate function lack of reserve for the constant and diagonal

* add memory reserve to recalculate
* add project_code dependency to make check
* remove m_padded_haplotypes
* make max_padded_read_lenght local
* make max_original_read_length reference clearer
* avoid checking all the reads a second time for padded_reads max length calculation
* add other to .gitignore for extra testdata