Consolidate entry points

[raymondcen]

• Added instructions and CLI flags for processing pre-classified .txt files using the --skip-classifier flag in classify_extract.py to both README.md and documentation/CONTRIBUTING.md. This allows users to extract from .txt files directly, with options for chunked extraction and label filtering. [1] [2]

• Updated the summary of extraction fields in documentation/CONTRIBUTING.md to remove references to the obsolete extract_from_txt.py and clarify that new fields should be added to classify_extract.py.

• Updated documentation/DESIGN_DECISIONS.md to document that extract_from_txt.py was merged into classify_extract.py as part of the new --skip-classifier workflow.

• Updated the test in tests/test_pdf_extraction.py to use sys.executable instead of hardcoding "python", ensuring the correct Python interpreter is used during test execution.

• Added a new sample file data/processed-text/test.txt for demonstration or testing purposes.

[Copilot]

Pull request overview

This PR consolidates the previously separate “extract from pre-classified .txt” workflow into the main classify_extract.py entry point (via --skip-classifier), updates documentation accordingly, and makes a small test robustness improvement.

Changes:

• Merged the former extract_from_txt.py pipeline into src/pipeline/classify_extract.py behind --skip-classifier, including label filtering and chunked extraction options.
• Updated docs (README.md, documentation/CONTRIBUTING.md, documentation/DESIGN_DECISIONS.md) to reflect the consolidated entry point and removal of the old script.
• Updated tests/test_pdf_extraction.py to invoke the CLI with sys.executable instead of hardcoding python.

Reviewed changes

Copilot reviewed 7 out of 7 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
src/pipeline/classify_extract.py	Adds --skip-classifier TXT extraction path and consolidates shared extraction/preprocess logic into one entry point.
src/pipeline/extract_from_txt.py	Removes the standalone TXT pipeline script now that its functionality is consolidated.
documentation/CONTRIBUTING.md	Documents the new TXT extraction usage/flags and updates guidance on where extraction fields are maintained.
README.md	Adds a CLI example for extracting from pre-classified .txt inputs using --skip-classifier.
documentation/DESIGN_DECISIONS.md	Records the design decision to merge the former extract-from-txt entry point into classify_extract.py.
tests/test_pdf_extraction.py	Uses sys.executable to ensure the test runs with the active interpreter.
data/processed-text/test.txt	Adds a sample .txt file intended for demonstration/testing.

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[Copilot]

Implemented in cac2c1b: replaced /data/processed-text/test.txt with a short synthetic, project-relevant predator-diet sample text.

[marknovak]

Retargeted base from main to dev so this merges into the integration branch first. The changes look clean — Copilot flagged 2 inline comments worth a quick look. Needs one human review before merge.

[marknovak]

This branch has merge conflicts with dev that need to be resolved before it can be merged. Please rebase merge-entry-points onto dev and fix the following:

Content conflicts:

• src/pipeline/classify_extract.py — both branches modified this file
• README.md
• documentation/CONTRIBUTING.md
• data/processed-text/test.txt

Modify/delete conflict:

• src/pipeline/extract_from_txt.py — this PR deletes it, but dev has modified it independently. You'll need to decide whether to carry dev's changes into classify_extract.py before deleting the file, or reconsider the deletion.

To rebase:

git fetch origin
git rebase origin/dev
# resolve conflicts, then:
git push --force-with-lease