docs: add "Choose your workflow" section to the README - #116
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Surface a goal-oriented "what should I run first?" map between the Quickstart and the full command reference, so new users can match an intent (look at a structure, sanity-check, compare, featurise, build a graph dataset, coarse-grain, triage docking, drive via MCP) to a starting command and an obvious next step. Also adds the `structure-report` and `prepare` commands to the command table (they existed but were undocumented there) and gives each an example.
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What
Improves feature discoverability in the README by adding a compact, goal-oriented "Choose your workflow" section between the Quickstart and the full command reference. It answers "what should I run first?" by mapping an intent to a starting command and an obvious next step:
molscope file.pdb/reportqc→structure-reportcomparepresets→analyzebuild_dataset/export→preparepresets→coarse-graindock-report(+dock-summary/dock-diverse/dock-rank)Also
Surfaces two commands that existed but were missing from the command table:
structure-report(protein ML-readiness) andprepare(train/val/test splits), each with an example in the CLI block. Internal anchor links (#command-line,#use-from-an-ai-assistant-mcp) verified.Docs-only change.