Improve shellcheck coverage

[edmorley]

• Switches to using git ls-files instead of a hardcoded list of scripts to lint (shellcheck doesn't support recursively scanning for scripts itself). This means a few files that were not previously linted now are, so need fixes.
• Adds a .shellcheckrc which is used to enable optional shellcheck checks via enable=all. Most of these checks either already passed or have been fixed in this PR - however, a few others need a closer look so have been disabled for now to reduce the size of this PR.
• As part of doing this I discovered an NLTK bug with setting NLTK_DATA after Misc bash script refactoring #1595, which has now been fixed. Since that change was not yet released, I've not mentioned the fix here in the changelog.

Shellcheck's optional checks as of v0.10.0:

$ shellcheck --list-optional
name:    add-default-case
desc:    Suggest adding a default case in `case` statements
example: case $? in 0) echo 'Success';; esac
fix:     case $? in 0) echo 'Success';; *) echo 'Fail' ;; esac

name:    avoid-nullary-conditions
desc:    Suggest explicitly using -n in `[ $var ]`
example: [ "$var" ]
fix:     [ -n "$var" ]

name:    check-extra-masked-returns
desc:    Check for additional cases where exit codes are masked
example: rm -r "$(get_chroot_dir)/home"
fix:     set -e; dir="$(get_chroot_dir)"; rm -r "$dir/home"

name:    check-set-e-suppressed
desc:    Notify when set -e is suppressed during function invocation
example: set -e; func() { cp *.txt ~/backup; rm *.txt; }; func && echo ok
fix:     set -e; func() { cp *.txt ~/backup; rm *.txt; }; func; echo ok

name:    check-unassigned-uppercase
desc:    Warn when uppercase variables are unassigned
example: echo $VAR
fix:     VAR=hello; echo $VAR

name:    deprecate-which
desc:    Suggest 'command -v' instead of 'which'
example: which javac
fix:     command -v javac

name:    quote-safe-variables
desc:    Suggest quoting variables without metacharacters
example: var=hello; echo $var
fix:     var=hello; echo "$var"

name:    require-double-brackets
desc:    Require [[ and warn about [ in Bash/Ksh
example: [ -e /etc/issue ]
fix:     [[ -e /etc/issue ]]

name:    require-variable-braces
desc:    Suggest putting braces around all variable references
example: var=hello; echo $var
fix:     var=hello; echo ${var}

See also:
https://github.com/koalaman/shellcheck/blob/master/shellcheck.1.md