Open-cravat

- Fix job database locking issues when quickly refreshing jobs
- Set default temporary file encoding to utf-8
- Put all job databases in WAL journal mode
- Further improve handling of modules with dependencies. Resolve circular dependencies and improve version resolution.
- Allow lowercase ref bases in input files. Cast bases to uppercase in results.
- Add support for filtering on user created notes.
- Remove filtering for certain vcf INFO columns

- Add annotation packages. Packages are bundled sets of annotators and filters designed to support common types on analysis
- Add metrics gathering. Anonymous metrics are collected and reported to KarchinLab. Metrics include information such as input format type, number of variants, annotators selected, and operating system. No indentifiable information is collected about the user, and no details of variants are reported.
- Inform users when installing large (>5 GB) modules through the GUI. Don't install modules if they are bigger than available disk space.
- Improve installation of modules with dependencies. Dependency chains longer than 2 are supported.
- Fix issues when running annotators which have dependencies
- Remove temp files by default in runs submitted through the GUI

- Change vcf parsing library to PyVCF3
- Change minimum python version to 3.8.x
- Conversion for gds format files. Allow converting binary input files.
- Fix toggling between and/or in query builder
- Improve reporting of errors in the command line, adding new `--debug` option to all commands.
- Cache system config file to reduce disk reads
- Improve handling of globs in input filenames
- Add new support email address