Miniwdl

`miniwdl run` ops refinements

* The run outputs JSON *for call cache hits* now refer to output files under the *newly created* `out/` run directory, rather than `out/` from the cached run
* These are usually just symbolic links to the same files; with config `[file_io] output_hardlinks`, they're hardlinks to the same inodes
* [Insourced](https://github.com/chanzuckerberg/miniwdl/tree/main/tools_image) the docker image used for HTTP URI downloads using aria2c
* Suppress the "running as root" warning when miniwdl is running inside a container

`miniwdl run` ops refinements

* Add option `[scheduler] fail_fast = false` to stop a workflow after a task failure *only after* letting other ongoing tasks finish normally
* In contrast to default behavior of immediately terminating all ongoing tasks
* Can be used with call caching to avoid necessarily discarding work in progress
* Improve compatibility with filesystems' varying support for "flock"
* With `--log-json`, produce *both* JSON and default log files in each run directory

With thanks to [CZI Science](https://chanzuckerberg.com/science/) and all these cheery faces!


The v0.11.x series will serve as the "release candidate" for miniwdl v1.0.0.

`miniwdl run`

* [WDL 1.1] `unzip()` function
* Under `out/` directory, add dotfiles helping a crawling program to distinguish `File` and `Directory` outputs

`miniwdl check`

* restore `--no-shellcheck` option (hidden) for compatibility

`WDL`

* Restore interpolation placeholder options (sep, default, true, false) as they're deprecated, not removed from WDL 1.1

`miniwdl check`

* Command-line option to suppress certain warning(s) globally: `--suppress Warning1,Warning2`
* `--suppress CommandShellCheck` replaces `--no-shellcheck`
* WDL 1.1 warnings for newly-deprecated coercions and placeholder options

`miniwdl run`

* [WDL `version 1.1`] accept input overrides for task runtime settings, e.g. `mytask.runtime.cpu=4`
* work around module import [race condition](https://bugs.python.org/issue41567) in python3.9
* add retry logic for some idempotent dockerd requests (complements task-level `maxRetries`)

`miniwdl configure`

* create `~/.config` if necessary

`import WDL`

* reminder: Python scripts now must explicitly import the `WDL.runtime` and `WDL.Lint` subpackages in order to use their functionality