v1.6.1

Refactor release. Implements ROADMAP Theme 6 (surface consolidation):
five tool clusters merge behind one canonical entry each, two
synthesis protocols collapse into a single parametrized form, and a
new deprecation telemetry pipeline (alias / redirect log +
tool_deprecations_summary) gives projects an audit trail before the
next MAJOR removes the back-compat layer. Every old name continues
to work end-to-end — the dispatcher injects the implied
operation / kind / source / mode / scope parameter and logs
the hit. See docs/MIGRATION.md for the full
old-name → new-invocation table.

Added — consolidated tools

• tool_search(query, source='auto'|'semantic_scholar'|'pubmed'|'crossref'|'arxiv'|'web', limit?) — replaces the five per-provider search tools. source='auto' (default) picks providers from the query domain (biomedical → S2 + PubMed; ML/methods → S2 + arXiv; social → Crossref + S2; geoscience → Crossref + arXiv; generic → web).
• tool_plan(operation='turn'|'advance'|'clear') — replaces tool_plan_turn / tool_plan_advance / tool_plan_clear. tool_plan_step_grounded stays standalone.
• sys_path(operation='create'|'abandon'|'list', ...) — replaces sys_path_create / sys_path_abandon / sys_path_list.
• tool_ground(mode='explicit'|'from_context', claim, ...) — replaces tool_grounding_register + tool_ground_from_context.
• tool_verify(scope='claim'|'project', ...) — replaces tool_claim_verify + tool_grounding_verify.
• tool_lessons(operation='record'|'consult', ...) — replaces tool_lessons_record + tool_lessons_consult.
• mem_log(kind='methods'|'decision'|'hypothesis'|'analysis', ...) — replaces mem_methods_append / mem_decision_log / mem_hypothesis_update / mem_analysis_log.
• tool_deprecations_summary — aggregates counts from .os_state/deprecations.log (alias hits + redirect-stub loads) by kind / source / target. Run before upgrading to the next MAJOR.

Added — protocol consolidation

• synthesis/printable.yaml — new parametrized protocol covering both poster (format='poster') and handout / one-pager (format='handout' / 'one_pager') variants. Quality bars, audience profiles, and steps branch on the format parameter.

Added — infrastructure

• Protocol loader honours redirect_to: <target> + redirect_params: {...}. The loader recursively resolves the target, attaches _redirected_from + _redirect_params to the result for AI context, and logs every redirect to .os_state/deprecations.log. Cycles are detected across the whole chain.
• Dispatcher logs every deprecated-alias invocation to .os_state/deprecations.log with kind='tool_alias'. A new _ALIAS_PARAM_INJECTION table injects the back-compat parameter so legacy call shapes keep working without the caller supplying the consolidation argument.
• Preflight adds two new checks: Alias table complete (every _ALIASES entry resolves to a registered handler; every _DEPRECATED_ALIASES entry has a param-injection row) and Redirect-stub targets resolve (every YAML with redirect_to: points at a real protocol; no stub carries both redirect_to: and steps:).
• Preflight: 15 → 17 checks. All green.
• docs/MIGRATION.md (new) — the complete migration table.

Improved

• _router_index.yaml (version 10 → 11): adds synthesis/printable entry; marks synthesis/synthesis_handout + synthesis/synthesis_poster as redirects in their summaries; updates the handout decomposition to point at the consolidated target.
• 44 new tests in tests/unit/test_v161_consolidation.py exercise alias completeness, param-injection coverage, end-to-end old-name behaviour, deprecation logging, redirect resolution, cycle detection, and the new preflight checks. Pytest 553 → 597 passes.

Migration table

Cluster	Old name	New invocation
Search	tool_search_semantic_scholar	tool_search(query=..., source='semantic_scholar')
Search	tool_search_pubmed	tool_search(query=..., source='pubmed')
Search	tool_search_crossref	tool_search(query=..., source='crossref')
Search	tool_search_arxiv	tool_search(query=..., source='arxiv')
Search	tool_search_web	tool_search(query=..., source='web')
Plan	tool_plan_turn	tool_plan(operation='turn')
Plan	tool_plan_advance	tool_plan(operation='advance')
Plan	tool_plan_clear	tool_plan(operation='clear')
Path	sys_path_create	sys_path(operation='create', name=..., hypothesis=...)
Path	sys_path_abandon	sys_path(operation='abandon', path_name=..., rationale=...)
Path	sys_path_list	sys_path(operation='list')
Ground	tool_grounding_register	tool_ground(mode='explicit', claim=..., sources=[...])
Ground	tool_ground_from_context	tool_ground(mode='from_context', claim=..., context_paths=[...])
Verify	tool_claim_verify	tool_verify(scope='claim', claim=..., verifications=[...])
Verify	tool_grounding_verify	tool_verify(scope='project')
Lessons	tool_lessons_record	tool_lessons(operation='record', outcome=..., reflection=...)
Lessons	tool_lessons_consult	tool_lessons(operation='consult', task=...)
Memory	mem_methods_append	mem_log(kind='methods', method=..., ...)
Memory	mem_decision_log	mem_log(kind='decision', context=..., selected=..., rationale=...)
Memory	mem_hypothesis_update	mem_log(kind='hypothesis', hypothesis_id=..., status=...)
Memory	mem_analysis_log	mem_log(kind='analysis', entry=...)
Protocol	synthesis/synthesis_handout	synthesis/printable (redirect_params: {format: handout})
Protocol	synthesis/synthesis_poster	synthesis/printable (redirect_params: {format: poster})

Compatibility: old names continue to work for the lifetime of
the current MAJOR. They are scheduled for removal in the next MAJOR.
Run tool_deprecations_summary to audit your project's exposure
before then.

Bumped

• version 1.6.0 → 1.6.1 in pyproject.toml, src/research_os/__init__.py, CITATION.cff.
• All 114 protocol YAMLs bumped 1.6.0 → 1.6.1 (semantic-routing embeddings rebuilt to track).
• _router_index.yaml version 10 → 11.

Counts

• Tools surface: 166 → 174 (+8 new consolidated tools; old names retained as aliases for back-compat).
• Protocols: 113 → 114 (+1 consolidated synthesis/printable; old handout + poster retained as redirect stubs).
• Active surface after consolidation (excluding deprecated aliases / redirect stubs): ~89 distinct tool entry points + ~112 distinct protocol entry points.

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