Fix various style and security issues in shell scripts:

[logological]

• Use -- so that variables or globs that expand to names with dashes don't become command-line options
• Use $(...) instead of legacy `...`
• Quote variables when necessary to prevent globbing
• Remove extraneous semicolons at ends of commands
• Remove extraneous invocations of cat
• Use built-in ${var//x/y} or ${var/%x/y} instead of echo $var | sed s/x/y/
• Use while true instead of while [ 1 ]
• Use -r with read to avoid mistaken interpretation of escape codes
• Use [:lower:] and [:upper:] instead of a-z and A-Z with tr to support non-ASCII characters