test + python-tools.sh: Fix toplevel "make all" fallout

After a pipeline change, CI now runs "make all" in a repo's root, which uncovers two problems:
1. The help integration test only succeeded as long CI didn't run "make all" before "make test". That way, the checked out repository lacked the generated __init__.py files needed for some modular subcommands to be fully loaded, and hence, the test should have failed. The entire machinery only worked because the subcommands in question are not not essential to building jw-pkg itself: "secrets" and "posix". So, this commit adapts the help integration test to the new reality.
2. Regarding python-tools.sh: Commit 55060486 satisfies yapf in some places of the source code, but in others not anylonger.  So patch python-tools.sh's newline handling again.
While not thematically similar, both fixes get baked into one commit to satisfy the requirement that every single commit needs to pass "make clean all check test" individually.
Signed-off-by: Jan Lindemann <jan@janware.com>

scripts/python-tools.sh

@@ -81,12 +81,12 @@ cmd_create_init()
 			echo "import `module_path $f` as $f"
 			__add_seen $f
 		done
-		echo
 	fi
 
 	if [ ${#seen[@]} -eq 0 ]; then
 		echo "__all__ = []"
 	else
+		echo
 		echo "__all__ = ["
 		for dst_type in ${!seen[@]}; do
 			echo "    \"$dst_type\","

test/integration/jw-pkg/help/test-expected.txt

@@ -163,12 +163,55 @@ options:
                    %{codename}, %{gnu-triplet}, %{os-cascade}, %{os-release},
                    %{pkg-ext} (default: %{cascade})
 ============= Running: jw-pkg.py --log-level info posix --help
-usage: jw-pkg.py posix [-h]
+usage: jw-pkg.py posix [-h]  ...
 
 Perform various operations on a distro through its POSIX utility interface
 
 options:
   -h, --help  show this help message and exit
+
+Available subcommands of posix:
+  
+    copy      Copy files
+    tar       Handle tar archives
+============= Running: jw-pkg.py --log-level info posix copy --help
+usage: jw-pkg.py posix copy [-h] [-o OWNER] [-g GROUP] [-m MODE] [-F] src dst
+
+Copy files
+
+positional arguments:
+  src                  Source file URI
+  dst                  Destination file URI
+
+options:
+  -h, --help           show this help message and exit
+  -o, --owner OWNER    Destination file owner (default: None)
+  -g, --group GROUP    Destination file group (default: None)
+  -m, --mode MODE      Destination file mode (default: None)
+  -F, --fixed-strings  Don't expand macros in <src> and <dst> (default: False)
+============= Running: jw-pkg.py --log-level info posix tar --help
+usage: jw-pkg.py posix tar [-h]  ...
+
+Handle tar archives
+
+options:
+  -h, --help  show this help message and exit
+
+Available subcommands of tar:
+  
+    x         Extract a tar archive
+============= Running: jw-pkg.py --log-level info posix tar x --help
+usage: jw-pkg.py posix tar x [-h] -f ARCHIVE_PATH dst
+
+Extract a tar archive
+
+positional arguments:
+  dst                   Destination root URI
+
+options:
+  -h, --help            show this help message and exit
+  -f, --archive-path ARCHIVE_PATH
+                        Archive path
 ============= Running: jw-pkg.py --log-level info projects --help
 usage: jw-pkg.py projects [-h]  ...
 
@@ -689,9 +732,93 @@ positional arguments:
 options:
   -h, --help  show this help message and exit
 ============= Running: jw-pkg.py --log-level info secrets --help
-usage: jw-pkg.py secrets [-h]
+usage: jw-pkg.py secrets [-h]  ...
 
 Manage package secrets
 
+options:
+  -h, --help            show this help message and exit
+
+Available subcommands of secrets:
+  
+    compile-templates   Compile package template files
+    install             Install secrets from various sources as static secrets
+                        onto the target
+    list-compilation-output
+                        List package compilation output files
+    list-secrets        List package secret files
+    list-templates      List package template files
+    rm-compilation-output
+                        Remove package compilation output files
+============= Running: jw-pkg.py --log-level info secrets compile-templates --help
+usage: jw-pkg.py secrets compile-templates [-h] [--owner OWNER]
+                                           [--group GROUP] [--mode MODE]
+                                           [packages ...]
+
+Compile package template files
+
+positional arguments:
+  packages           Package names (default: None)
+
+options:
+  -h, --help         show this help message and exit
+  --owner, -o OWNER  Default output file owner (default: None)
+  --group, -g GROUP  Default output file group (default: None)
+  --mode, -m MODE    Default output file mode (default: None)
+============= Running: jw-pkg.py --log-level info secrets install --help
+usage: jw-pkg.py secrets install [-h] [--only-missing] src [packages ...]
+
+Install secrets from various sources as static secrets onto the target
+
+positional arguments:
+  src             URI of secret source
+  packages        Package names (default: None)
+
+options:
+  -h, --help      show this help message and exit
+  --only-missing  Install only secrets not already on the target (default:
+                  False)
+============= Running: jw-pkg.py --log-level info secrets list-compilation-output --help
+usage: jw-pkg.py secrets list-compilation-output [-h] [--all] [packages ...]
+
+List package compilation output files
+
+positional arguments:
+  packages    Package names (default: None)
+
+options:
+  -h, --help  show this help message and exit
+  --all       Show all output targets, including non-existent files (default:
+              False)
+============= Running: jw-pkg.py --log-level info secrets list-secrets --help
+usage: jw-pkg.py secrets list-secrets [-h] [--all] [packages ...]
+
+List package secret files
+
+positional arguments:
+  packages    Package names (default: None)
+
+options:
+  -h, --help  show this help message and exit
+  --all       Show all secret paths, including non-existent files (default:
+              False)
+============= Running: jw-pkg.py --log-level info secrets list-templates --help
+usage: jw-pkg.py secrets list-templates [-h] [packages ...]
+
+List package template files
+
+positional arguments:
+  packages    Package names (default: None)
+
+options:
+  -h, --help  show this help message and exit
+============= Running: jw-pkg.py --log-level info secrets rm-compilation-output --help
+usage: jw-pkg.py secrets rm-compilation-output [-h] [packages ...]
+
+Remove package compilation output files
+
+positional arguments:
+  packages    Package names (default: None)
+
 options:
   -h, --help  show this help message and exit