research-workflow-orchestrator

research-workflow-orchestrator

Coordinate an entire research project without turning consequential scientific decisions into silent automation. The orchestrator resumes from .research/workflow_state.yml, performs safe work automatically, and asks for one structured decision only when the next action crosses a declared gate.

This is a coordination skill, not a new research engine. It routes to the existing research-hub skills and available CLI/MCP integrations. Read references/workflow-contract.md before the first run. Read references/tool-adapters.md only for the current stage or when selecting a tool adapter. The machine-readable state contract is references/workflow-state.schema.json.

Use when

• The user asks to run, resume, automate, or supervise a multi-stage research project.
• Work spans at least three of topic scoping, discovery, synthesis, design, experiments, writing, and release.
• A persistent human-in-the-loop audit trail is required.

Do not use for one isolated operation. Route a single literature table to literature-triage-matrix, one design conversation to research-design-helper, one paper summary to paper-summarize, or project orientation alone to research-project-orienter.

Shared research contract

Read ../research-hub/references/research-protocol.md for the scope-to-query map, literature roles, version/decision observations and bounded completion; read ../research-hub/references/source-claim-audit.md for source support. Native research remains available when Hub runtime/actions are unavailable. Do not infer substantive coverage from a candidate count or command exit. If shared files are unavailable, preserve user constraints, actual source level, load-bearing evidence gaps and planned/executed distinctions explicitly.

Required inputs

1. Project root.
2. User objective and constraints.
3. Existing .research/ manifests, if present.
4. Available tool capabilities. Discover them; never assume an MCP server, connector, credential, or browser session exists.

If the state file does not exist, propose a workflow ID and start at orient. Creating the local state file is reversible, but present the initial plan before executing later stages.

Automation policy

Classify every proposed action before invoking a tool:

Action class	Default behavior
Read-only discovery, validation, comparison	Run automatically
Local deterministic generation with a preview or rollback	Run automatically, preserve provenance
Local reversible metadata update	Run automatically when inside approved scope
External write, public communication, account change	Stop at external_write
Costly or long experiment/simulation	Stop at experiment_authorization
Semantic manuscript/rebuttal change	Stop at semantic_revision
Submission, publication, release, merge, destructive cleanup	Stop at release_authorization

Unknown risk is gated. Tool availability never lowers the gate class.

Run loop

1. Load .research/workflow_state.yml and validate the fields used by the current run. If absent, initialize from the schema; do not invent completed decisions or artifacts.
2. Orient with research-project-orienter, or create a previewed local manifest using research-context-compressor after presenting the initial plan. This reversible project-local initialization needs no separate gate; freezing its research question or scope still needs scope_commitment.
3. Plan the smallest next stage. Name inputs, expected artifacts, tool adapter, validation, risk class, and any gate.
4. Decide:
   • no gate: execute and validate;
   • gate: show the decision packet and wait;
   • missing capability: use the documented fallback or report a blocker.
5. Record stage, action, hashes/provenance, validation result, and decision. Write state atomically; never record success before validation passes.
6. Advance only when exit criteria in the workflow contract pass. Otherwise retry within the declared bound or stop with a concrete blocker.
7. Resume from the recorded pending action. Never rerun a costly or external action merely because a new chat/session started.

Human decision packet

At a gate, present only what the researcher needs to decide:

Gate: <gate id>
Decision: <one sentence>
Why now: <evidence and uncertainty>
Proposed action: <tool + exact mutation/cost/scope>
Preview: <diff, plan, candidates, or artifact link>
Reversible: <yes/no and rollback>
Options: accept / decline / revise / cancel

• accept: record approval for the exact action and scope, then continue.
• decline: record the decision, choose a safe alternative if one exists, and do not repeatedly ask for the same rejected action.
• revise: block execution until a replacement action with a new hash is presented and accepted.
• cancel: record cancellation and stop the workflow cleanly.

An accept is valid only through a signed policy checkpoint or exact local-TTY hash confirmation. A bare actor label from an agent or MCP caller is not human authorization.

Approval is scoped to the described action. A later public, destructive, more expensive, or semantically different action needs a new decision.

Stage routing

Stage	Primary routes	Required evidence before advancing
orient	research-project-orienter, research-context-compressor	project manifest and open questions
scope	gap-to-topic, research-design-helper	accepted question, criteria, constraints
discover	literature-triage-matrix, research-hub search, Zotero	need-to-query coverage and actual outcomes, deduplicated candidate set, unresolved scope/access limits
synthesize	paper-summarize, paper-memory-builder, NotebookLM verifier	version/source-level claim-evidence map, assessed/total claims, contradictions and unassessed gaps
design	research-design-helper	design dossier and explicit assumptions
execute	project-specific code/experiment tools	reproducible command, outputs, validation
write	academic writing skill chain	source-linked draft and review findings
release	verification, Git/GitHub/submission tools	release checklist and human authorization

Do not synthesize claims from unverified metadata or treat a NotebookLM brief as ground truth. Do not invent missing sources, results, approvals, or tool output.

State and provenance

• Canonical state path: .research/workflow_state.yml.
• Store artifact paths plus SHA-256, stage, and timestamp. Do not store artifact contents in state.
• Store action IDs, exact scope, parameter/preview hashes, resource bounds, and decision summaries—not private deliberation or credentials. Execute an accepted action only when these machine-verifiable fields still match.
• Store every attempt and validation result in actions[]; terminal completed/cancelled states have no pending action, and cancelled must include a cancel decision.
• Keep pending_action specific enough to resume, but never include API keys, cookies, OAuth tokens, or secrets.
• If current bytes, dependencies, or time-sensitive inputs differ from the recorded evidence, rerun only the smallest affected validation.

Failure behavior

• Bound retries per action; default maximum is two attempts unless the plan declares a smaller limit.
• On repeated failure, set status to blocked, preserve the last verified artifact, and report the exact recovery condition.
• Never silently switch data sources, models, research questions, or inclusion criteria.
• Never treat an unavailable MCP tool as permission to perform a broader browser or shell mutation.

Completion output

Return:

1. current stage and status;
2. completed stages and validated artifacts;
3. human decisions and their scope;
4. unresolved evidence gaps or blockers;
5. exact next action, or none when complete.

The workflow is complete only when the release exit criteria pass or the user explicitly ends the project. A draft alone is not completion.

Executable runtime

Use the domain service through either interface; both paths make the same state transition:

• CLI: research-hub workflow init|status|validate|decide|resume|migrate
• MCP: workflow_initialize, workflow_status, workflow_validate, workflow_decide, workflow_resume, and workflow_migrate

All CLI operations accept --json. Migration is a dry run unless --apply is given; apply creates a backup and atomically replaces the state. Schema 1.0 remains readable, while decisions and resume require migration to schema 1.1.

The optional agent-collab-harness v0.4 policy/checkpoint layer is discovered at runtime. If no policy is configured, research-hub keeps its standalone behavior. If a policy is configured but the package, policy, or checkpoint is unavailable, resume fails closed. research-hub doctor --json reports the integration as available, unavailable, or misconfigured.