task runtime: revise input file mounting scheme

[mlin]

Mount the input files under the container working directory, so that they're always in a directory to which the command has read/write access, even though the individual files are (by default) read-only. Then the task can create files alongside the index files and output them (e.g. samtools/tabix index files).

Mount all input files into one flat directory to the extent possible (barring filename collisions), also improving compatibility with index file handling assumptions.

Expose copy_input_files through run_local_workflow and CLI.

[coveralls]

Pull Request Test Coverage Report for Build 1155

• 25 of 25 (100.0%) changed or added relevant lines in 1 file are covered.
• 15 unchanged lines in 1 file lost coverage.
• Overall coverage increased (+0.008%) to 96.946%

---

Files with Coverage Reduction	New Missed Lines	%
WDL/runtime/task.py	15	95.51%

Totals
Change from base Build 1148:	0.008%
Covered Lines:	4381
Relevant Lines:	4519

---

💛 - Coveralls