Caper

* Bug fixes
- Localization fails if a JSON, TSV or CSV file is not updated

> **IMPORTANT**: `--deepcopy` has been deprecated. Deepcopy is enabled by default and can be disabled with `--no-deepcopy`. `--use-singularity` and `--use-docker` are deprecated. Instead, `--singularity` and `--docker` can work as flags.

* Deprecated parameters
- `--deepcopy`: Deepcopy is enable by default. `--no-deepcopy` is added to disable it.
- `--use-docker`: `--docker` can work as a flag
- `--use-singularity`: `--singularity` can work as a flag

* New parameters
- `--no-deepcopy`: to disable deepcopy
- `--dry-run`: Caper creates all temporary files but does not take any action.

* New subcommand
- `debug`: an alias of `troubleshoot`, which is too long to type.

* Bug fixes
- Fixed all deepcopy-related bugs

* change of default parameters
- `db-timeout`: 10000 to 30000 (ms)
- `java-heap-run`: 2G to 2G
- `java-heap-server`: 8G to 7G

* added a subcommand `debug` , which is identical to `troubleshoot`.

* bug fix for `db` key error when `--no-file-db` or `-n` is given but `--file-db` or `-d` is defined
* update doc for `sbatch` command
- added `-export=ALL` to `sbatch` command to respect all environment variables (e.g. Conda activated `PATH`)

* added `--db-timeout` to give longer time for Cromwell to connect to DB.
- to prevent `db - Connection is not available` error even when no Caper/Cromwell process is attached to the DB file
- this error can happen when DB file is large
- default: `10000` (ms)

* upgrade google API from `v1` to `v2`: to fix PAPI 10 error
* added `--gcp-zones` to specify GCP zones to provision worker instances
- e.g. `--gcp-zones us-central1-b,us-west1-b`