v3.1.0

MINOR release. Backwards-compatible: every existing tool keeps its name + schema
(new capability is added via new operations/scopes and a new alias). Driven by a
fresh 11-area discovery audit of the 3.0.0 codebase.

Added

• Compiled routing sidecar (_route_meta.json). Routing no longer parses the
  104K _router_index.yaml at runtime. build_embeddings.py compiles a compact,
  comments-free JSON mirror (protocols/shortcut_intents/hierarchy + pre-baked
  tier + workflow_shape) that router.py and semantic.py share via a single
  load. It parses ~300× faster (~0.42 ms vs ~126 ms) and removes the per-route
  protocol-body reads. The YAML stays the authoring source; --route-meta-only
  rebuilds the sidecar without fastembed. New preflight gate validates the sidecar
  is fresh + consistent + embeddings-parity-checked.
• tool_verify(scope='outputs') — the "did the work actually land?" gate.
  Resolves a protocol's declared expected_outputs against the filesystem
  (glob-aware) and reports each present / empty / missing with a next_action.
  The injected protocol-completion step now requires it before logging
  completed, so the system refuses to call a missing or empty file "done".
  docs/VERSIONING.md documents the in-project versioning convention.
• sys_path(operation='rename') — give a generic analysis step a meaningful
  label. Keeps the NN_ lineage number, renames the folder, and re-points every
  downstream data/* symlink that targeted it. sys_step is now an alias for
  sys_path (the clearer name for numbered steps).
• Routing-targets preflight gate — every next_protocol / on_failure /
  see_also must point at a real protocol (dangling links were previously silent).

Improved

• Figures. tool_figure_palette('accent') now returns the exact RO_PALETTE
  colours apply_research_os_style applies (a hand-coloured figure matches an
  auto-styled one); adds diverging_emphasis. audit_figure_quality runs its
  text-overlap + default-font (DejaVu) legibility scan on a PNG's sibling SVG too,
  and a corrupt/empty image now warns instead of crashing the audit.
• Synthesis deliverables. tool_typst_compile archives the prior render to
  synthesis/archive/<name>_<timestamp>.pdf before overwriting (no silent
  clobber), flags single-page-target overflow (poster/cover-letter rendered to

  1 page = content overflowed — where overlapping text shows up), and counts
  pages without the off-by-one /Type /Pages miscount. The poster check no longer
  false-blocks scaffold-authored posters (#headline / #block-section).

• Wizard. Ctrl+C/Ctrl+D mid-wizard exits cleanly instead of a traceback; the
  "already exists" check moved to the start (no more filling out the whole wizard
  to be rejected at the end); email + ORCID inputs are format-validated.
• Doctrine. power_analysis replaced its data-shape→test-family menu with
  scaffold form (name the dimensions that fix the test, justify the choice).

Fixed

• state_freshness_check read workspace/state.json — a file that never exists —
  so the staleness signal was permanently dead; now reads the real ledger.
• get_dag_path / add_dag_node stopped persisting the constant
  execution_dag_path back into the ledger every call (write churn + schema noise).
• Dead-end pause detection read protocol_name but the execution log writes
  protocol — the signal was silently dead.
• Autopilot gate used str.lstrip('./') (strips characters), so .synthesis/x
  was mangled into synthesis/x and falsely gated; now strips the prefix properly.
• Maintainer docs (CLAUDE.md) pointed at the long-gone src/research_os/server.py
  monolith — repointed to the server/ package; dropped stale protocol counts.

Bumped

• version → 3.1.0 (pyproject / __init__ / CITATION); router index counter → 27.

Deferred (tracked for a future release)

• Tool-cluster consolidation (SLURM 4→1) — aliased, low user-visible benefit.
• A first-class renamable BRANCH object + retro-organization of loose work
  (higher-risk state-schema change beyond the step rename shipped here).
• Deeper audit-gate hardening (claims-gate-on-by-default, ship-gate
  rerun-resolution) — behavior-changing, staged separately.

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