CLI output path is hardcoded, making scripted usage difficult

[mustafagoktugibolar]

Problem

I've been using run_pageindex.py as part of a larger script that processes
multiple documents. The issue is that the output path is hardcoded to
./results/{name}_structure.json with no way to override it.

This becomes a problem when:

• Running the script from a different working directory
• Processing multiple documents into separate output folders
• Integrating into a pipeline where the output location needs to be controlled externally

Expected Behavior

Users should be able to specify where the output file is written via CLI arguments.

Proposed Solution

Add --output-dir and --output-file arguments:

# Write to a custom directory
python run_pageindex.py --pdf_path doc.pdf --output-dir /path/to/output

# Write to a specific file
python run_pageindex.py --pdf_path doc.pdf --output-file /path/to/result.json

Backward Compatibility

No breaking changes. If neither argument is provided, the output is still written
to ./results/{name}_structure.json — exactly the same as before.

[Copilot]

Pull request overview

Adds CLI configurability for where run_pageindex.py writes its JSON output, addressing scripted/pipeline usage where a hardcoded ./results/... path is inconvenient.

Changes:

• Added --output-dir and --output-file CLI flags (mutually exclusive) to control output location.
• Updated PDF and Markdown flows to write JSON to either the specified directory or explicit file path.
• Documented the new flags in README.md.

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 3 comments.

File	Description
run_pageindex.py	Adds mutually exclusive output path CLI args and updates both PDF/MD save logic to respect them.
README.md	Documents the new --output-dir / --output-file options in the optional parameters list.

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[Copilot]

Pull request overview

Copilot reviewed 2 out of 2 changed files in this pull request and generated no new comments.