Fix automated tests

[XPerianer]

• bumps checkout@v2 to checkout@v3, as checkout@v2 uses deprecated nodejs12 version
• checks for all files that are written by pcal script, and reruns it if one is missing Previously, we only checked for one specific file.

[github-actions[bot]]

:white_check_mark: Result of Pytest Coverage

---------- coverage: platform linux, python 3.8.14-final-0 -----------	Name	Stmts	Miss	Cover
gpucsl/init.py	0	0	100%
gpucsl/main.py	8	8	0%
gpucsl/cli/init.py	0	0	100%
gpucsl/cli/cli.py	48	3	94%
gpucsl/cli/cli_io.py	59	26	56%
gpucsl/cli/cli_util.py	9	1	89%
gpucsl/cli/command_line_parser.py	15	0	100%
gpucsl/pc/init.py	0	0	100%
gpucsl/pc/discover_skeleton_discrete.py	51	0	100%
gpucsl/pc/discover_skeleton_gaussian.py	52	0	100%
gpucsl/pc/edge_orientation/init.py	0	0	100%
gpucsl/pc/edge_orientation/edge_orientation.py	12	0	100%
gpucsl/pc/edge_orientation/orientation_rules.py	52	1	98%
gpucsl/pc/edge_orientation/v_structures.py	20	0	100%
gpucsl/pc/gaussian_device_manager.py	174	1	99%
gpucsl/pc/helpers.py	82	1	99%
gpucsl/pc/kernel_management.py	198	15	92%
gpucsl/pc/pc.py	49	5	90%
gpucsl/pc/pc_validations.py	31	10	68%
TOTAL	860	71	92%
=================	71	passed,	74