analyze-codebase-workflow

# Analyze Codebase Workflow Survey an arbitrary repository to auto-detect data flows, file I/O, and script dependencies, then produce a structured annotation plan for manual refinement. ## When to Use - Onboarding onto an unfamiliar codebase and need to understand data flow - Starting putior integration in a project that has no PUT annotations yet - Auditing an existing project's data pipeline before documentation - Preparing an annotation plan before running `annotate-source-files` ## Inputs - **Required**: Path to the repository or source directory to analyze - **Optional**: Specific subdirectories to focus on (default: entire repo) - **Optional**: Languages to include or exclude (default: all detected) - **Optional**: Detection scope: inputs only, outputs only, or both (default: both + dependencies) ## Procedure ### Step 1: Survey Repository Structure Identify source files and their languages to understand what putior can analyze. ```r library(putior) # List all supported languages and their extensions list_supported_languages() list_supported_languages(detection_only = TRUE) # Only languages with auto-detection # Get supported extensions exts <- get_supported_extensions() ``` Use file listing to understand repo composition: ```bash # Count files by extension in the target directory find /path/to/repo -type f | sed 's/.*\.//' | sort | uniq -c | sort -rn | head -20 ``` **Got:** A list of file extensions present in the repo, with counts. Map these against `get...