Refactor docker usage and support input files

[jrm5100]

Running cargo run --release --example docker

Does an ls on the /volA mount in one execution then cats the contents of the file in the next execution, showing support for:

• Input files (non-local kinds like s3 are still todo!)
• Persistent volumes across executions

Reply: Reply { executions: Some(NonEmpty { head: ExecutionResult { status: 0, stdout: "test_input.txt\n", stderr: "" }, tail: [ExecutionResult { status: 0, stdout: "Hello, world from an input\n", stderr: "" }] }) }
Reply: Reply { executions: Some(NonEmpty { head: ExecutionResult { status: 0, stdout: "test_input.txt\n", stderr: "" }, tail: [ExecutionResult { status: 0, stdout: "Hello, world from an input\n", stderr: "" }] }) }
Reply: Reply { executions: Some(NonEmpty { head: ExecutionResult { status: 0, stdout: "test_input.txt\n", stderr: "" }, tail: [ExecutionResult { status: 0, stdout: "Hello, world from an input\n", stderr: "" }] }) }
Reply: Reply { executions: Some(NonEmpty { head: ExecutionResult { status: 0, stdout: "test_input.txt\n", stderr: "" }, tail: [ExecutionResult { status: 0, stdout: "Hello, world from an input\n", stderr: "" }] }) }
Reply: Reply { executions: Some(NonEmpty { head: ExecutionResult { status: 0, stdout: "test_input.txt\n", stderr: "" }, tail: [ExecutionResult { status: 0, stdout: "Hello, world from an input\n", stderr: "" }] }) }
Reply: Reply { executions: Some(NonEmpty { head: ExecutionResult { status: 0, stdout: "test_input.txt\n", stderr: "" }, tail: [ExecutionResult { status: 0, stdout: "Hello, world from an input\n", stderr: "" }] }) }
Reply: Reply { executions: Some(NonEmpty { head: ExecutionResult { status: 0, stdout: "test_input.txt\n", stderr: "" }, tail: [ExecutionResult { status: 0, stdout: "Hello, world from an input\n", stderr: "" }] }) }
Reply: Reply { executions: Some(NonEmpty { head: ExecutionResult { status: 0, stdout: "test_input.txt\n", stderr: "" }, tail: [ExecutionResult { status: 0, stdout: "Hello, world from an input\n", stderr: "" }] }) }
Reply: Reply { executions: Some(NonEmpty { head: ExecutionResult { status: 0, stdout: "test_input.txt\n", stderr: "" }, tail: [ExecutionResult { status: 0, stdout: "Hello, world from an input\n", stderr: "" }] }) }
Reply: Reply { executions: Some(NonEmpty { head: ExecutionResult { status: 0, stdout: "test_input.txt\n", stderr: "" }, tail: [ExecutionResult { status: 0, stdout: "Hello, world from an input\n", stderr: "" }] }) }

[jrm5100]

I'd imagine there may be a lot of room to make it more efficient (especially for large files) but at least we have a working example here so we could theoretically do a samtools flagstat or something.

Specifically we re-copy all of the inputs before each execution, even though those in the volumes could be checked to ensure they weren't modified first.

[claymcleod]

Pending @peterhuene's comment, this looks good.