v3.0.0

MAJOR release. Research OS now fits the shape of your work — classic
linear analysis, iterative tool/software building, lightweight exploration,
notebook-driven analysis, or a multi-study program — instead of assuming one
shape. Alongside the modes it turns several "advertised but unenforced"
rigor promises into enforced ones, overhauls routing for both beginners and
deep-critic PIs, and improves every protocol.

Added — Workspace modes

• workspace.mode in researcher_config.yaml (+ research-os init --workspace-mode, and a wizard "What are you building?" step):
  analysis (default, unchanged) · tool_build · exploration ·
  notebook · multi_study. A SCAFFOLD_PROFILES registry scaffolds each
  shape; state, router, and audits dispatch on the active mode.
• tool_build mode — Research OS governs an inner project from above:
  spec/ + decisions/ (ADRs) + eval/ (the harness that defines "done")
  • milestones.md + governance.md, with the tool itself in an inner dir
    that gets its OWN git init. "Done" = tests + build + eval pass.
• build/ protocol family — spec_and_design → implement_iteration
  (loop) → test_strategy → benchmark_vs_baseline → release_and_changelog.
  Plus exploration/ (triage → loop → promote-to-step) and notebook/ +
  program/ orienting protocols.
• tool_git (inner-repo version control; commits stamped with the RO
  step for provenance), tool_build (configured build/test/lint
  runner), and tool_audit(scope='tool', dimension=tests|git_hygiene|build).

Added — Rigor that is actually enforced

• tool_finalize_project — a server ship-gate that HARD-BLOCKS "done"
  on unresolved audit blockers, cited-but-invalid PDFs, ungrounded numbers,
  or stub sections, unless a logged researcher override clears it.
• PDF integrity — literature downloads are validated by the %PDF-
  magic header; a renamed 403/HTML page is deleted + recorded, never counted
  as a paper. Every PDF count uses magic validation, not glob("*.pdf").
• Substrate-checked grounding — tool_verify now checks a claim against
  its cited file (a number is "verified" only if the source actually
  contains it; self-asserted support becomes "unverified").

Added — Beginner ↔ PI gradient

• tool_explain — a layered, grounded tutor (intuition → mechanics →
  caveats → when-not-to-use → reading list) for any skill level.
• tool_deliverable_chooser — an output_types-gated "I'm done, what
  now?" on-ramp.
• Mode-scoped tool listing — the per-turn catalog shrinks from 151 to
  ~113–128 tools.
• Router overhaul — beginner-vocabulary layer ("i have a csv what do i
  do", "make a chart", "is my result significant"), a confidence-margin gate
  that asks instead of confidently misrouting, capped reckless single-word
  triggers, mode-aware routing bias, and workflow_shape as a routing signal.

Improved

• Every protocol swept for doctrine compliance: hardcoded thresholds /
  method menus / canned step sequences replaced with "name-the-dimension +
  cite-the-source" scaffolds; scope-tag mislabels fixed; see_also
  cross-links added.
• Typst deliverables compile across all 12 venues (uniform template/conf).
• Audits read the real synthesis/paper.typ (dual Typst + Markdown), so the
  rigor gates no longer silently no-op.
• New researcher docs: TOOL_BUILDER.md, a beginner on-ramp in START.md,
  workspace modes documented across the guides.
• New scripts/lint_coherence.py preflight gate: docs/templates can no
  longer reference a removed tool or hand-write a tool/protocol count.

Fixed

• All 7 IDE rule templates + docs purged of removed-tool references
  (tool_plan_*, tool_synthesize/dashboard/figure, tool_grounding_*).
• synthesis_check no longer reports success on a message-less error.
• 11 broken documentation cross-references.

Behaviour changes that may affect existing projects (why this is MAJOR)

• A project with placeholder/HTML files named *.pdf will see them no
  longer counted as literature — the literature gate may newly fire (add a
  real PDF, or override with a rationale).
• tool_finalize_project can refuse to finalize a project with unresolved
  blockers; previously every blocker was advisory.
• tool_verify returns unverified for self-asserted claims that do not
  resolve to a cited source.
• New field workspace.mode defaults to analysis; existing projects keep
  classic behaviour with no change.

Migration

• Analysis projects upgrade with no changes (mode defaults to analysis,
  byte-identical scaffold). Re-run research-os init --refresh to pick up
  the updated AGENTS.md / IDE rules.
• The planned tool-cluster consolidations (merging the SLURM / exec / route
  families; sys_path → sys_step) are deferred to 3.1.0 and will ship with
  aliases so no call site breaks.

---