fix(flex): use sql_upgrade.php CLI mode in upgradeOpenEMR

The previous implementation rewrote sql_upgrade.php with sed to inject the
source version. After openemr/openemr#11906 added native CLI support, the
target sed pattern (`$form_old_version = $_POST['form_old_version'];`) no
longer exists in sql_upgrade.php — the assignment is now
`$form_old_version = $cliFromVersion ?? ($_POST['form_old_version'] ?? '')`.

The sed becomes a silent no-op, leaving `$form_old_version = ''`. The loop
guard `strcmp($version, '') < 0` is then false for every upgrade file, so
sql_upgrade.php starts processing from `2_6_0-to-2_6_1_upgrade.sql` instead
of the requested 5.0.0. That file contains an unguarded
`INSERT INTO categories_seq VALUES (0)` which adds a second row alongside
the demo dump's `(26)`. Several files later,
`5_0_0-to-5_0_1_upgrade.sql:407` runs
`UPDATE categories_seq SET id = (SELECT MAX(id) FROM categories)` without a
WHERE clause; with two rows being set to the same id, the second hits a
PRIMARY KEY violation and the upgrade aborts. The database is left at
v5.0.0 with only the earliest upgrade scripts partially applied — visible
to users as broken login CSS, missing columns
(`lists_medication.reporting_source_record_id`), and erroring background
services after `openemr-cmd drid`.

Switch to the supported `--from=VERSION` CLI argument, which is honored by
the loop guard at `sql_upgrade.php:379`
(`!empty($_POST['form_submit']) || $cliFromVersion !== null`) and removes
the need to mutate the script source.

Validated end-to-end: `openemr-cmd drid` now leaves the database at
v8.1.1-dev / v_database=538, with `categories_seq` containing the expected
single row and `lists_medication.reporting_source_record_id` present.

Assisted-by: Claude Code

Author: kojiromike

docker/openemr/flex/utilities/devtoolsLibrary.source

@@ -207,26 +207,14 @@ demoData() {
 # ============================================================================
 
 # Upgrades OpenEMR database from a specified version to the current version.
-# This function runs OpenEMR's sql_upgrade.php script programmatically
-# by modifying it to run non-interactively.
+# Invokes sql_upgrade.php in CLI mode (added in openemr/openemr#11906).
 #
 # Parameters:
 #   $1: Original OpenEMR version (e.g., "5.0.0", "6.0.0")
 #
-# Process:
-#   1. Creates a temporary version of sql_upgrade.php
-#   2. Modifies it to run non-interactively (auto-submit form)
-#   3. Sets the source version
-#   4. Executes the upgrade script
-#   5. Cleans up temporary file
-#
 # Must call prepareVariables() before calling this function.
 upgradeOpenEMR() {
-    sed -e "s@!empty(\$_POST\['form_submit'\])@true@" < /var/www/localhost/htdocs/openemr/sql_upgrade.php > /var/www/localhost/htdocs/openemr/sql_upgrade_temp.php
-    sed -i "s@\$form_old_version = \$_POST\['form_old_version'\];@\$form_old_version = '${1}';@" /var/www/localhost/htdocs/openemr/sql_upgrade_temp.php
-    sed -i "1s@^@<?php \$_GET['site'] = 'default'; ?>@" /var/www/localhost/htdocs/openemr/sql_upgrade_temp.php
-    php -f /var/www/localhost/htdocs/openemr/sql_upgrade_temp.php
-    rm -f /var/www/localhost/htdocs/openemr/sql_upgrade_temp.php
+    php -f /var/www/localhost/htdocs/openemr/sql_upgrade.php -- --from="${1}"
 }
 
 # ============================================================================