update examples

grammar: fix tokenization of "runtime", "meta", and "parameter_meta" (c…

…hanzuckerberg#363 @DavyCats)

polish runner docs

fix size() given a null input

improve Map type inference (chanzuckerberg#332)

factor out type unification logic shared with Array & IfThenElse

addresses chanzuckerberg#256

allow subworkflow name in input JSON key

To supply an optional input for a subworkflow call, Cromwell input JSON expects the key to include (i) the workflow name, (ii) the call name, (iii) the subworkflow name, and finally (iv) the input name. The need to include (iii) the subworkflow name is questionable, as discussed on openwdl/wdl#340

This change makes miniwdl accept such inputs either with or without the subworkflow name, by removing it if it's present. To ensure unambiguous resolution, also forbids collision between a call's name and that of its containing workflow.

chanzuckerberg#193

exit from CLI.main

reorganize applied tests and add encode_atac_seq

run CI builds as non-root user (chanzuckerberg#293)

It's useful to run the test suite as some arbitrary uid so that the runner has realistic file permissions constraints.

runner: use docker image's $SHELL to interpret task command