I wanted to make a script to check if updated flatpak app permissions have changed before updating them. I decided to use ChatGPTs newest model, 01-preview for this task and holy crap am I impressed. I had to give it 14 commands to get to the final product and it seems to work great. That number could have been reduced quite a bit had I done things a bit differently.

I still had to find the problems, look up reference docs to correct it, and even debug in an IDE a little. But just telling it where the problems were, it got there in the end, and its user interaction output is way better than what I was planning on doing.

Sections:

My final updated copy of the script
List of the changes I made from the AI produced script
The commands I gave the AI
The final script the AI produced

<?php
// -- This script checks for Flatpak updates and reports permission changes. --

// Function to parse permissions from Flatpak metadata
function parsePermissions($content) {
    $permissions = [];
    $lines = is_array($content) ? $content : explode("\n", $content);
    $currentSection = '';
    $skipSections = ['Application']; // Sections to skip

    foreach ($lines as $line) {
        $line = trim($line);

        if (empty($line)) {
            continue;
        }

        // Check for section headers
        if (preg_match('/^\[(.*)\]$/', $line, $matches)) {
            $currentSection = $matches[1];

            // Skip the [Application] section
            if (in_array($currentSection, $skipSections)) {
                $currentSection = '';
                continue;
            }

            $permissions[$currentSection] = [];
        } elseif ($currentSection !== '') {
            // Only process lines within non-skipped sections
            $parts = explode('=', $line, 2);
            if (count($parts) == 2) {
                $key = $parts[0];
                $values = explode(';', trim($parts[1], ';'));
                $permissions[$currentSection][$key] = $values;
            } else {
                // Handle keys without '=' (e.g., single permissions)
                $permissions[$currentSection][$line] = [];
            }
        }
    }

    return $permissions;
}

// Function to compare permissions
function comparePermissions($current, $new) {
    $differences = [];

    // Get all sections
    $sections = array_unique(array_merge(array_keys($current), array_keys($new)));

    foreach ($sections as $section) {
        $currentSection = isset($current[$section]) ? $current[$section] : [];
        $newSection = isset($new[$section]) ? $new[$section] : [];

        // Get all keys in this section
        $keys = array_unique(array_merge(array_keys($currentSection), array_keys($newSection)));

        foreach ($keys as $key) {
            $currentValues = isset($currentSection[$key]) ? $currentSection[$key] : [];
            $newValues = isset($newSection[$key]) ? $newSection[$key] : [];

            // Compare values
            $added = array_diff($newValues, $currentValues);
            $removed = array_diff($currentValues, $newValues);

            if (!empty($added) || !empty($removed)) {
                $differences[$section][$key] = [
                    'added' => $added,
                    'removed' => $removed,
                ];
            }
        }
    }

    return $differences;
}

// Function to output a line with appId (if given), colored red (IsError=true) or green (IsError=false)
function outputColor($appId, $str, $isError=true, $NoNewline=false)
{
    // Determine if coloring should be used
    static $hasColors=null;
    if(!isset($hasColors)) {
        $hasColors=stream_isatty(STDOUT) && (!trim(`command -v tput`) || intval(`tput colors`)>=16);
    }

    echo
        (!$hasColors ? '' : ($isError ? "\e[31m" : "\e[32m")).
        ($appId ? "$appId: " : '').
        $str.
        (!$hasColors ? '' : "\e[0m").
        ($NoNewline ? '' : "\n");
}

// Function to display permission differences
function displayDifferences($appId, $differences) {
    outputColor($appId, 'Permission changes:');
    foreach ($differences as $section => $keys) {
        outputColor(null, "  [$section]");
        foreach ($keys as $key => $changes) {
            if (!empty($changes['added'])) {
                outputColor(null, "    + $key = " . implode(';', $changes['added']));
            }
            if (!empty($changes['removed'])) {
                outputColor(null, "    - $key = " . implode(';', $changes['removed']));
            }
        }
    }
    echo "\n";
}

// Function to ask the user a question
function askQuestion($Question) {
    outputColor('', "$Question (y/N): ", true, true);
    $handle = fopen('php://stdin', 'r');
    $line = fgets($handle);
    $answer = trim(strtolower($line));
    fclose($handle);
    return ($answer == 'y' || $answer == 'yes');
}

// Get architecture (moved above the loop)
$archCommand = 'flatpak --default-arch';
exec($archCommand, $archOutput);
$arch = trim(implode('', $archOutput));

// Step 1: Get the list of installed Flatpaks
$installedCommand = 'flatpak list -a --columns=application,branch,origin,options';
exec($installedCommand, $installedOutput);

// Remove header line if present
if (!empty($installedOutput) && strpos($installedOutput[0], 'Application ID') !== false) {
    array_shift($installedOutput);
}

// Build an associative array of installed applications
$installedApps = [];

foreach ($installedOutput as $line) {
    // The output is tab-delimited
    $columns = explode("\t", trim($line));
    if (count($columns) >= 4) {
        $appId = $columns[0];
        $branch = $columns[1];
        $origin = $columns[2];
        $options = $columns[3];

        $installedApps[$appId] = [
            'appId' => $appId,
            'branch' => $branch,
            'origin' => $origin,
            'options' => $options,
        ];
    }
}

// Get the list of updates
exec('echo n | flatpak update', $updatesOutput);
foreach ($updatesOutput as $Line) {
    if (preg_match('/^ *\d+\.\s+([\w\.-]+)/', $Line, $matches)) {
        $updatesAvailable[]=$matches[1];
    }
}

// Let the user confirm the updates
echo str_repeat('-', 80)."\n";
echo implode("\n", $updatesOutput)."\n";
echo str_repeat('-', 80)."\n";
if (empty($updatesAvailable)) {
    outputColor('', 'No updates available for installed Flatpaks.');
    exit(0);
}
if (!askQuestion('Found '.count($updatesAvailable).' updates. Continue?')) {
    echo "Updates canceled.\n";
    exit(0);
}

$permissionChanges = [];
foreach ($updatesAvailable as $appId) {
    if (!isset($installedApps[$appId])) {
        outputColor($appId, 'Installed app not found. Skipping.');
        continue;
    }

    $app = $installedApps[$appId];
    $branch = $app['branch'];
    $origin = $app['origin'];
    $options = $app['options'];

    // Determine if it's an app or runtime
    $isRuntime = strpos($options, 'runtime') !== false;

    // Paths to the metadata files
    if ($isRuntime) {
        $metadataPath = "/var/lib/flatpak/runtime/$appId/$arch/$branch/active/metadata";
    } else {
        $metadataPath = "/var/lib/flatpak/app/$appId/$arch/$branch/active/metadata";
    }

    // Check if the metadata file exists
    if (!file_exists($metadataPath)) {
        outputColor($appId, 'Metadata file not found. Skipping.');
        continue;
    }

    // Read current permissions from the metadata file
    $metadataContent = file_get_contents($metadataPath);
    $currentPermissions = parsePermissions($metadataContent);

    // Get new metadata from remote
    $ref = $appId . '/' . $arch . '/' . $branch;
    $remoteInfoCommand = 'flatpak remote-info --show-metadata ' . escapeshellarg($origin) . ' ' . escapeshellarg($ref);

    // Clear $remoteOutput before exec()
    $remoteOutput = [];
    exec($remoteInfoCommand, $remoteOutput);

    if (empty($remoteOutput)) {
        outputColor($appId, 'Failed to retrieve remote metadata. Skipping.');
        continue;
    }

    // Parse new permissions from the remote metadata
    $newPermissions = parsePermissions($remoteOutput);

    // Compare permissions
    $differences = comparePermissions($currentPermissions, $newPermissions);

    if (!empty($differences)) {
        $permissionChanges[$appId] = $differences;
        displayDifferences($appId, $differences);
    } else {
        outputColor($appId, 'No permission changes found.', false);
    }
}

// If there are no permission changes, inform the user
if (empty($permissionChanges)) {
    echo "No permission changes detected in the available updates.\n";
}

// Ask user if they want to proceed
if (askQuestion('Do you want to proceed with the updates?')) {
    // Proceed with updates
    echo "Updating Flatpaks...\n";
    passthru('flatpak update -y');
} else {
    echo "Updates canceled.\n";
}
?>

• Added “outputColor” function and wrapped appropriate echo statements into it
• Added “-a” to “flatpak list”
• Added output line “Installed app not found. Skipping”
• Added output line “No permission changes found.”
• Added “askQuestion” function since there are now multiple places in the script that ask questions
• Changed get-updates command from “flatpak remote-ls --updates” to “echo n | flatpak update” (with a regex extraction). Also now confirms the update list with the user.

For demonstration purposes, I have left all of my original typos uncorrected below.

<?php
/**
 * This script checks for Flatpak updates and reports permission changes.
 */

// Function to parse permissions from Flatpak metadata
function parsePermissions($content) {
    $permissions = [];
    $lines = is_array($content) ? $content : explode("\n", $content);
    $currentSection = '';
    $skipSections = ['Application']; // Sections to skip

    foreach ($lines as $line) {
        $line = trim($line);

        if (empty($line)) {
            continue;
        }

        // Check for section headers
        if (preg_match('/^\[(.*)\]$/', $line, $matches)) {
            $currentSection = $matches[1];

            // Skip the [Application] section
            if (in_array($currentSection, $skipSections)) {
                $currentSection = '';
                continue;
            }

            $permissions[$currentSection] = [];
        } elseif ($currentSection !== '') {
            // Only process lines within non-skipped sections
            $parts = explode('=', $line, 2);
            if (count($parts) == 2) {
                $key = $parts[0];
                $values = explode(';', trim($parts[1], ';'));
                $permissions[$currentSection][$key] = $values;
            } else {
                // Handle keys without '=' (e.g., single permissions)
                $permissions[$currentSection][$line] = [];
            }
        }
    }

    return $permissions;
}

// Function to compare permissions
function comparePermissions($current, $new) {
    $differences = [];

    // Get all sections
    $sections = array_unique(array_merge(array_keys($current), array_keys($new)));

    foreach ($sections as $section) {
        $currentSection = isset($current[$section]) ? $current[$section] : [];
        $newSection = isset($new[$section]) ? $new[$section] : [];

        // Get all keys in this section
        $keys = array_unique(array_merge(array_keys($currentSection), array_keys($newSection)));

        foreach ($keys as $key) {
            $currentValues = isset($currentSection[$key]) ? $currentSection[$key] : [];
            $newValues = isset($newSection[$key]) ? $newSection[$key] : [];

            // Compare values
            $added = array_diff($newValues, $currentValues);
            $removed = array_diff($currentValues, $newValues);

            if (!empty($added) || !empty($removed)) {
                $differences[$section][$key] = [
                    'added' => $added,
                    'removed' => $removed,
                ];
            }
        }
    }

    return $differences;
}

// Function to display permission differences
function displayDifferences($appId, $differences) {
    echo "Permission changes for $appId:\n";
    foreach ($differences as $section => $keys) {
        echo "  [$section]\n";
        foreach ($keys as $key => $changes) {
            if (!empty($changes['added'])) {
                echo "    + $key = " . implode(';', $changes['added']) . "\n";
            }
            if (!empty($changes['removed'])) {
                echo "    - $key = " . implode(';', $changes['removed']) . "\n";
            }
        }
    }
    echo "\n";
}

// Get architecture (moved above the loop)
$archCommand = 'flatpak --default-arch';
exec($archCommand, $archOutput);
$arch = trim(implode('', $archOutput));

// Step 1: Get the list of installed Flatpaks
$installedCommand = 'flatpak list --columns=application,branch,origin,options';
exec($installedCommand, $installedOutput);

// Remove header line if present
if (!empty($installedOutput) && strpos($installedOutput[0], 'Application ID') !== false) {
    array_shift($installedOutput);
}

// Build an associative array of installed applications
$installedApps = [];

foreach ($installedOutput as $line) {
    // The output is tab-delimited
    $columns = explode("\t", trim($line));
    if (count($columns) >= 4) {
        $appId = $columns[0];
        $branch = $columns[1];
        $origin = $columns[2];
        $options = $columns[3];

        $installedApps[$appId] = [
            'appId' => $appId,
            'branch' => $branch,
            'origin' => $origin,
            'options' => $options,
        ];
    }
}

// Get the list of available updates
$updatesCommand = 'flatpak remote-ls --updates --columns=application';
exec($updatesCommand, $updatesOutput);

// Remove header line if present
if (!empty($updatesOutput) && strpos($updatesOutput[0], 'Application ID') !== false) {
    array_shift($updatesOutput);
}

// Build a list of applications that have updates
$updatesAvailable = array_map('trim', $updatesOutput);

if (empty($updatesAvailable)) {
    echo "No updates available for installed Flatpaks.\n";
    exit(0);
}

$permissionChanges = [];

foreach ($updatesAvailable as $appId) {
    if (!isset($installedApps[$appId])) {
        // The updated app is not in the installed apps list, skip it
        continue;
    }

    $app = $installedApps[$appId];
    $branch = $app['branch'];
    $origin = $app['origin'];
    $options = $app['options'];

    // Determine if it's an app or runtime
    $isRuntime = strpos($options, 'runtime') !== false;

    // Paths to the metadata files
    if ($isRuntime) {
        $metadataPath = "/var/lib/flatpak/runtime/$appId/$arch/$branch/active/metadata";
    } else {
        $metadataPath = "/var/lib/flatpak/app/$appId/$arch/$branch/active/metadata";
    }

    // Check if the metadata file exists
    if (!file_exists($metadataPath)) {
        echo "Metadata file not found for $appId. Skipping.\n";
        continue;
    }

    // Read current permissions from the metadata file
    $metadataContent = file_get_contents($metadataPath);
    $currentPermissions = parsePermissions($metadataContent);

    // Get new metadata from remote
    $ref = $appId . '/' . $arch . '/' . $branch;
    $remoteInfoCommand = 'flatpak remote-info --show-metadata ' . escapeshellarg($origin) . ' ' . escapeshellarg($ref);

    // Clear $remoteOutput before exec()
    $remoteOutput = [];
    exec($remoteInfoCommand, $remoteOutput);

    if (empty($remoteOutput)) {
        echo "Failed to retrieve remote metadata for $appId. Skipping.\n";
        continue;
    }

    // Parse new permissions from the remote metadata
    $newPermissions = parsePermissions($remoteOutput);

    // Compare permissions
    $differences = comparePermissions($currentPermissions, $newPermissions);

    if (!empty($differences)) {
        $permissionChanges[$appId] = $differences;
        displayDifferences($appId, $differences);
    }
}

// If there are no permission changes, inform the user
if (empty($permissionChanges)) {
    echo "No permission changes detected in the available updates.\n";
}

// Ask user if they want to proceed
echo "Do you want to proceed with the updates? (y/N): ";
$handle = fopen("php://stdin", "r");
$line = fgets($handle);
$answer = trim(strtolower($line));

if ($answer == 'y' || $answer == 'yes') {
    // Proceed with updates
    echo "Updating Flatpaks...\n";
    passthru('flatpak update -y');
} else {
    echo "Updates canceled.\n";
}

fclose($handle);
?>

Since I have been moving my primary workstation to Linux, I have been in need of finding a new password manager after Roboform failed me. I decided to try out KeePassXC but was having trouble since my Ungoogled Chromium browser was sandboxed in Flatpak. The instructions for this on Unix Stack Exchange were no longer working so I had to dig into it myself.

The 2 primary problems were that:
1) The browsers’ sandboxes did not have the QT libs.
2) The interprocess communication pipe socket had been renamed from kpxc_server to org.keepassxc.KeePassXC.BrowserServer.

The following are the instructions to get KeePassXC running in Flatpak versions of both Chrome and Firefox. This was tested on Linux Mint 21.3 with both Ungoogled Chromium and Firefox. You will need to change the KP_FLATPAK_PACKAGE if you use other versions of Chrome.

1. Run the relevant below environment variables in your command shell before running the commands in the following steps:
   

   #Shared environment variables:
   KP_CUSTOM=/home/$USER/keepass-browser
   KP_JSON_NAME=org.keepassxc.keepassxc_browser.json
   
   #Chrome environment variables:
   KP_FLATPAK_PACKAGE=io.github.ungoogled_software.ungoogled_chromium
   KP_JSON_START=~/.config/chromium/NativeMessagingHosts
   KP_JSON_END=~/.var/app/$KP_FLATPAK_PACKAGE/config/chromium/NativeMessagingHosts
   
   #Firefox environment variables:
   KP_FLATPAK_PACKAGE=org.mozilla.firefox
   KP_JSON_START=~/.mozilla/native-messaging-hosts
   KP_JSON_END=~/.var/app/$KP_FLATPAK_PACKAGE/.mozilla/native-messaging-hosts
   		

2. Install and enable the browser extension:
   KeePassXD > Tools > Settings > Browser Integration:
   
   • Check “Enable Browser Integration”
   • Check “Chromium” and/or “Firefox”
   • Download the plugin listed on this screen in your browser
   • Click "OK"
   Note: This creates $KP_JSON_START/$KP_JSON_NAME
   
   
3. Set up the needed files in the sandbox:
   

   #Put KeePass proxy and needed library files in user directory
   mkdir -p $KP_CUSTOM/lib
   mkdir -p $KP_JSON_END #Needed for firefox
   cp /usr/bin/keepassxc-proxy $KP_CUSTOM/
   rsync -a /usr/lib/x86_64-linux-gnu/libicudata* /usr/lib/x86_64-linux-gnu/libicuuc* /usr/lib/x86_64-linux-gnu/libicui* /usr/lib/x86_64-linux-gnu/libdouble* /usr/lib/x86_64-linux-gnu/libsodium* /usr/lib/x86_64-linux-gnu/libQt5* $KP_CUSTOM/lib
   
   #Copy the JSON file to the Flatpak app directory and change the executable path in the file
   cp $KP_JSON_START/$KP_JSON_NAME $KP_JSON_END/
   sed -i "s/\/usr\/bin\//"$(echo $KP_CUSTOM | sed 's_/_\\/_g')"\//" $KP_JSON_END/$KP_JSON_NAME
   		

4. Add permissions to the Flatpak:
   

   flatpak override --user --filesystem=$KP_CUSTOM:ro $KP_FLATPAK_PACKAGE #Only required if home directory is not shared to the Flatpak
   flatpak override --user --filesystem=xdg-run/org.keepassxc.KeePassXC.BrowserServer:ro $KP_FLATPAK_PACKAGE
   flatpak override --user --env=LD_LIBRARY_PATH=$(flatpak info --show-permissions $KP_FLATPAK_PACKAGE | grep -oP '(?<=LD_LIBRARY_PATH=).*')";$KP_CUSTOM/lib" $KP_FLATPAK_PACKAGE