refactor: standardize file permissions to 0644 for data files

[luoliwoshang]

• Many files were using os.ModePerm which gives execute permissions (0777) to JSON, config, and source files
• Data files like .json and .cfg shouldn't have execute permissions

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 84.20%. Comparing base (3f82aa9) to head (6f5c40f).

Additional details and impacted files

@@ Coverage Diff @@## main #520 +/- ##
=======================================
Coverage 84.20% 84.20% =======================================
Files 27 27 Lines 2747 2747 =======================================
Hits 2313 2313 Misses 391 391 Partials 43 43 

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