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Fix/citation list inputs - #132

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lfoppiano wants to merge 2 commits into
fix/converter-duplicate-linksfrom
fix/citation-list-inputs
Open

lfoppiano wants to merge 2 commits into
fix/converter-duplicate-linksfrom
fix/citation-list-inputs

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…lity

New tests cover main(), the JSON/Markdown companions, error markers in
subdirectories, directory batching, citation lists, request error mapping
and the logging configuration. Two of them exposed defects:

- requests' exceptions derive from IOError, so a timeout or connection
  error was caught by the "failed to open file" handler and recorded as a
  400 marker with a misleading message. The handlers are now ordered most
  specific first and ReadTimeout maps to 408 as intended.
- PDFs were eligible inputs for processCitationList and were read as text
  by process_txt. That service now only accepts .txt files.
Any .txt was an eligible input for processCitationList, including the
<stem>_<status>.txt markers written next to the inputs when no output
directory is given. A rerun posted the previous run's markers as citation
lists, producing marker-of-marker files and inflated counts. PDFs are no
longer eligible for this service either, since process_txt reads them as
text and fails.
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