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Secure Execution

The Secure Execution orchestrator (secure_run.sh) is an alternative launch point to the standard pipeline. It is a superset orchestrator: it executes the standard pipeline seamlessly, but then appends critical steganographic and cryptographic payloading post-processes.

Verified Multi-Project Results

Post-processing is the same for every workspace returned by discover_projects(). Representative row (control-positive exemplar):

Project Pages Overlays Barcodes Metadata XMP Manifest
code_project varies by manuscript build ✅ ✅ ✅ ✅ ✅

All other active projects/ names: _generated/active_projects.md. Anything under projects_archive/ or projects_in_progress/ is not processed until moved into projects/.

The secure_run.sh script discovers all active projects and processes each one in sequence. Steganographic outputs include:

  • *_steganography.pdf — augmented PDF with overlays, barcodes, and metadata
  • *.hashes.json — SHA-256/512 hash manifest sidecar

Interactive Mode

If you run ./secure_run.sh with no arguments, you enter an interactive UI (similar to ./run.sh).

The UI immediately details your active infrastructure/config/secure_config.yaml parameters and allows you to select which permutation to run (Fast, Core, Full, etc) with Steganography automatically affixed at the end.

Project Selection

By default, secure_run.sh will target all discovered projects.

If you wish to only run the pipeline on one project, press p in the interactive menu, type the index number of the project you wish to target, and hit Enter. The subsequent run will only generate and secure PDFs for that singular project.

Non-Interactive (CLI) Mode

For automated deployments or rapid iteration, secure_run.sh supports standard pipeline bypass flags:

# Run the pipeline across all projects, but skip the LLM queries and infrastructure test bottlenecks
./secure_run.sh --project all --skip-infra --core-only --pipeline
# Don't run the pipeline at all, just search for existing PDF files and apply Steganography to them for the specific code_project
./secure_run.sh --project code_project --steganography-only

Full Flag List

Flag Effect
--project <name> Select a specific project, or omit to run a multi-project sweep.
--pipeline Bypasses the UI completely and automatically commences running.
--skip-infra Skips running the infra_tests/ suite (Stage 3 bottleneck).
--core-only Skips running the requires_ollama LLM processing loop (Stage 7/8 bottleneck).
--steganography-only Skips pipeline execution completely and only performs the Steganography loops.