fix(shell): all remaining shellcheck issues

[kojiromike]

Short description of what this resolves:

Fixes all shellcheck warnings when running with -oall (maximum strictness) across docker/openemr (7.0.4+), packages/standard, and utilities.

Changes proposed in this pull request:

Shell style improvements:

• Quote variables to prevent word splitting (SC2086)
• Use find -exec {} + instead of find -print0 | xargs -0
• Use arithmetic syntax (( )) instead of [ ] for numeric comparisons
• Use single = in [[ ]] tests instead of ==
• Use single quotes for literal strings
• Use mkdir -p instead of [[ ! -d ]] && mkdir
• Use POSIX parameter expansion for optional args: ${VAR:+-flag} ${VAR:+"$VAR"}
• Use : instead of true for no-op commands
• Use echo for simple strings, printf only when format specifiers needed
• Replace manual ANSI escapes with tput

Bug fixes:

• Fix misplaced quote in chown command (7.0.4, 8.0.0 devtoolsLibrary.source)

Legitimate shellcheck disables with comments:

• SC2086: CONFIGURATION variable intentionally word-splits (see fix(docker): auto_configure.php inconsistency between flex and other versions #539)
• SC2154: Variables passed as environment variables to container
• SC2310: Functions in retry loops with set -e are intentional
• SC2016: Literal $ in warning messages

AI disclosure:

• Yes, I used AI to help with this PR

[jesdynf]

@bradymiller I don't think this is exceptional and I've spot-checked it (and tested things on the commandline until I got what it was trying to get across) but it touches every script we own. Is there anything you want to peek at it before we let it through?

[bradymiller]

Will this require this change (both for 7.0.3 and 7.0.4) if not already there:

openemr-devops/docker/openemr/flex-edge/auto_configure.php

Lines 27 to 48 in 8f3eca7

	// Collect parameters(if exist) for installation configuration settings
	for ($i=1; $i < count($argv); $i++) {
	if ($argv[$i] == '-f' && isset($argv[$i+1])) {
	// Handle case where a single string contains all parameters
	$configString = $argv[$i+1];
	$configPairs = preg_split('/\s+/', trim($configString));
	foreach ($configPairs as $pair) {
	if (strpos($pair, '=') !== false) {
	list($index, $value) = explode('=', $pair, 2);
	$installSettings[$index] = $value;
	}
	}
	// Skip the next argument since we already processed it
	$i++;
	} else {
	// Handle standard key=value parameters
	$indexandvalue = explode("=", $argv[$i]);
	$index = $indexandvalue[0];
	$value = $indexandvalue[1] ?? '';
	$installSettings[$index] = $value;
	}
	}

[kojiromike]

bah, there was a bug in my git ls-files and this didn't actually catch all the shellcheck issues. There are still a ton in the xbackup scripts.

[jesdynf]

Those might not be worth fighting. I need to migrate away from the current MySQL image with Percona's XtraBackup stuff to something with MariaDB.

[jesdynf]

@kojiromike I've migrated off the xbackup stuff, which was blocking you, but this pull is aging -- should we close or can we move on it?

[kojiromike]

I'll move on it soon.