Enable ruff PTH (flake8-use-pathlib) and fix all findings

Replaces os.path/open()/os.stat()/os.chmod() calls with their Path
method equivalents across src, tests, misc, and bin, wrapping str
variables in Path(...) where they must stay str for other uses (e.g.
subprocess argv, CLI-arg formatting). helpers.safe_symlink() now
decodes StrOrBytesPath to a str Path via os.fsdecode() upfront, same
pattern already used elsewhere for the str|bytes union.

misc/pdf_text_diff.py

@@ -23,7 +23,7 @@ def main(
     engine: Annotated[str, cyclopts.Parameter()] = 'pdftotext',
 ):
     """Compare text in PDFs."""
-    with open(pdf1, 'rb') as f1, open(pdf2, 'rb') as f2:
+    with pdf1.open('rb') as f1, pdf2.open('rb') as f2:
         text1 = run(
             ['pdftotext', '-layout', '-', '-'],
             stdin=f1,