Add warning if a local work dir is found

[KevinSayers]

Description

Workflow managers commonly create a local working directory which can be sizable. When quickly developing a workflow and running locally this work dir can be created, and when run later with AGC the dir can end up being uploaded. This can make it seem like AGC hangs as it is bundling and uploading this data.

Use Case

When switching between local workflow runs and using AGC to submit to Batch.

Proposed Solution

Check if the workflow being uploaded has a common workflow work dir such as .nextflow or .snakemake, and provide a warning message to the user if one is found.

Other information

[rforsyth]

Sounds like a good feature to add. We will include it in the backlog.

[KevinSayers]

Looks like this idea has been floated before #414 discussion seems to be include a .agc-ignore file which can have these work dirs.