Replace PHASE__ and STAGE__ column schema with step column

[alyssadai]

Change allows input imaging bagels to be fully long format

• step column should be required and have no missing values (?)

• remove HAS_DATATYPE__ and HAS_IMAGE__ columns for now (this info will probably be part of a different file in Nipoppy, or added back with different column names in future)

• remove MissingValue column property

• remove the has_mri_data column

• use pipeline-version-step instead of pipeline-version for tracking completion

• update plot of records x pipeline status so every pipeline-version-step combination has a separate bar

• update READMEs

• update QPN data files

  • was the nipoppy/qpn repo moved?

• double check status descriptions

• keep the incomplete / unavailable statuses

Q's:

• corresponding changes in phenotypic file identifier columns, to make sure they are named the same way? yes