apps: tweaks to be more robust and prevent the stupid flood of 'sh: 0: getcwd() failed: No such file or directory' when running an app upgrade/remove from /var/www/$app, sometimes making it look like the upgrade failed when it didnt

src/service.py

@@ -688,13 +688,15 @@ def _get_services():
     ]
     for name in services_with_package_condition:
         package = services[name]["ignore_if_package_is_not_installed"]
-        if os.system(f"dpkg --list | grep -q 'ii *{package}'") != 0:
+        if check_output(f"dpkg-query --show --showformat='${{db:Status-Status}}' '{package}' 2>/dev/null || true") != "installed":
             del services[name]
 
     php_fpm_versions = check_output(
-        r"dpkg --list | grep -P 'ii  php\d.\d-fpm' | awk '{print $2}' | grep -o -P '\d.\d' || true"
+        r"dpkg --list | grep -P 'ii  php\d.\d-fpm' | awk '{print $2}' | grep -o -P '\d.\d' || true",
+        cwd="/tmp"
     )
     php_fpm_versions = [v for v in php_fpm_versions.split("\n") if v.strip()]
+
     for version in php_fpm_versions:
         # Skip php 7.3 which is most likely dead after buster->bullseye migration
         # because users get spooked

src/utils/system.py

@@ -159,7 +159,7 @@ def ynh_packages_version(*args, **kwargs):
 
 
 def dpkg_is_broken():
-    if check_output("dpkg --audit") != "":
+    if check_output("dpkg --audit", cwd="/tmp/") != "":
         return True
     # If dpkg is broken, /var/lib/dpkg/updates
     # will contains files like 0001, 0002, ...