use localized filenames for File inputs used in expressions in Non-Input Declarations

[notestaff]

Currently, the spec says: "When a WDL author uses a File input in their Command Section, the fully qualified, localized path to the file is substituted into the command string." But if a File input is used in an expression on the right-hand side of a non-input declaration, the substitution is not done. Is there a reason for this?

[mlin]

cf. https://github.com/broadinstitute/cromwell/issues/5540 https://github.com/openwdl/wdl/issues/371

[jdidion]

Localized paths should also be used when evaluating private variables. If the spec doesn't already say this then we should add that explicitly.