deep-research-workflow

name	deep-research-workflow
description	Use when a research task benefits from an explicit phased workflow with structured source handoff across search, analysis, and writing, and when preserving citations across phases matters.
metadata	{"short-description":"Phased deep research with structured citations"}

Deep Research Workflow

Windows Runtime Commands

On native Windows, use the managed Windows runner and the native runtime command target. Set $runtime to the installed runtime root. Multi-agent installs usually use %LOCALAPPDATA%\ai-agents-skills\runtime. Then run:

$runtime = if ($env:AAS_RUNTIME_ROOT) { $env:AAS_RUNTIME_ROOT } else { "$env:LOCALAPPDATA\ai-agents-skills\runtime" }
& "$runtime\run_skill.bat" "skills/deep-research-workflow/run_deep_research_workflow.bat" <args>

PowerShell-first runners can use the native PowerShell command target:

& "$runtime\run_skill.ps1" "skills/deep-research-workflow/run_deep_research_workflow.ps1" <args>

POSIX examples below use run_skill.sh and .sh command targets; use the Windows command target above on native Windows.

This skill provides a Codex-native phased research workflow:

1. search
2. analyze
3. write

Use it when the user wants a deeper research pass than a normal quick synthesis and when source preservation matters.

For any writing-producing output, load writing-style-settings.md before the write phase. For mathematical manuscripts, TCS reports, graph-theoretic drafts, formal-proof prose, or LaTeX output, also load math-manuscript-style.md. Finalizable reports must record style_profile_ref, policy_hash, active_overlays, active_requirement_ids, and style_applied in the run ledger or final artifact metadata.

Minimal runtime helper

Initialize a deep-research scaffold with:

bash "$AAS_RUNTIME_ROOT/run_skill.sh" \
  skills/deep-research-workflow/run_deep_research_workflow.sh init --dir /path/to/workspace

For machine-checkable research runs, initialize structured ledgers too:

bash "$AAS_RUNTIME_ROOT/run_skill.sh" \
  skills/deep-research-workflow/run_deep_research_workflow.sh init --structured --dir /path/to/workspace

For research where formal verification may help, initialize the optional v2 formal lane:

bash "$AAS_RUNTIME_ROOT/run_skill.sh" \
  skills/deep-research-workflow/run_deep_research_workflow.sh init --structured --schema-version 2 --formal --dir /path/to/workspace

Validate the structured ledgers before delivery with:

bash "$AAS_RUNTIME_ROOT/run_skill.sh" \
  skills/deep-research-workflow/run_deep_research_workflow.sh validate --dir /path/to/workspace/research

Validate a v2/formal workspace with:

bash "$AAS_RUNTIME_ROOT/run_skill.sh" \
  skills/deep-research-workflow/run_deep_research_workflow.sh validate --schema-version 2 --dir /path/to/workspace/research

Verify the helper setup with:

bash "$AAS_RUNTIME_ROOT/run_skill.sh" \
  skills/deep-research-workflow/run_deep_research_workflow.sh doctor

Run the offline strict workflow smoke with:

bash "$AAS_RUNTIME_ROOT/run_skill.sh" \
  skills/deep-research-workflow/run_deep_research_workflow.sh selftest

selftest validates named positive and negative v2 scenarios for finalizable delivery, AGD evidence, weak computation rejection, formal promotion, and artifact-ref safety. It is the preferred runtime smoke for serious-research installs.

When to use

• deep topic research
• report-style synthesis
• research with explicit citation preservation
• tasks where search, interpretation, and final writing should be kept separate

Routing boundary

Prefer source-research for lightweight browse-and-synthesize work.

Prefer this skill when:

• the user wants an explicit phased workflow
• you need a structured handoff between search, analysis, and writing
• preserving source linkage across phases is part of the task quality bar

When not to use

• simple factual lookups
• casual current-events questions where a normal browse-and-answer flow is sufficient
• local-paper retrieval tasks already covered by zotero or calibre
• requests that only ask to investigate, diagnose, review, audit, verify, or report, unless the user explicitly asks for a phased workflow or durable research artifacts

Workflow

Phase 1 — Search

Inputs:

• user question or topic

• any seed URLs, papers, datasets, or constraints

• gather relevant sources

• prefer primary sources when practical

• record source metadata with stable S1, S2, ... identifiers

• separate observed facts from tentative interpretations

Outputs:

• a source ledger
• optional sources.jsonl records for machine validation
• stable S* source ids
• initial claim candidates
• noted coverage gaps

Use these templates when helpful:

• installed template deep-research-sources

Zotero cross-check

Between Phase 1 and Phase 2, treat every paper-like source as a library-check task:

• search the local library with zotero
• assign exactly one verification status
• preserve that status in the source ledger

Allowed status values:

• [IN_LIBRARY] — confirmed and found in Zotero
• [NOT_IN_LIBRARY] — confirmed paper, not present in Zotero
• [NOT_A_PAPER] — blog post, docs page, forum thread, dataset page, or similar non-paper source
• [UNVERIFIED] — claimed as a paper, but existence or identity could not be confirmed

Do not mark a source as verified based only on appearance or title shape. If identity remains unclear, keep [UNVERIFIED].

For v2 finalizable delivery, every paper-like source that supports a final claim must also record library_check_tool, library_checked_at, and library_check_ref.

Phase 2 — Analyze

Inputs:

• the source ledger from Phase 1, including Zotero verification status

• any extracted document structure or database records

• group findings into themes

• identify conflicts, uncertainties, and gaps

• preserve the source mapping for each important claim

• keep S* ids stable across all phases

• note which claims are strongly supported and which are provisional

Outputs:

• a theme matrix
• claim-to-source mapping
• optional claims.jsonl records for machine validation
• uncertainty notes
• candidate open problems or next-step questions
• optional figure opportunities with proposed F* ids and supporting S* ids

Detailed handoff structure:

• references/source-handoff.md
• installed template deep-research-analysis

Research quality guards

For nontrivial, delegated, or completeness-claiming research, record guard outputs before final synthesis:

• ScopeGuard for scope drift and exclusions
• EvidenceGuard for claim-to-source or claim-to-evidence linkage
• VerifyGuard for readiness checks separate from final delivery judgment
• BudgetGuard for parent-owned token, USD, depth, and hop limits
• RegressionGuard for load-bearing workflow text and template contracts

Use the closed schema in references/research-quality-guards.md. Do not use a single aggregate research quality score. Structured runs record these as guards.jsonl.

For v2 ready and ready-with-caveats, delivery is finalizable only when the run has non-blocking EvidenceGuard and VerifyGuard outputs, at least one supported claim, a checked report evidence record, current model freshness metadata in model_freshness.json, and no blocking guard gaps. Use v1 only for compatibility workflows that do not claim those serious-research guarantees.

Optional formal verification lane

Use the formal lane only when it fits the research object. Lean formalization is optional because many graph theory and combinatorics proofs are too expensive or under-supported to formalize during a normal research pass.

For v2 structured runs, formal artifacts live under formal/:

• formal_targets.jsonl records which claims are formalization candidates, required formal checks, and promotion state.
• statement_equivalence_reviews.jsonl records whether the informal claim and formal statement are equivalent enough to use as evidence.
• artifacts/ stores Lean skeletons, candidate Lean files, typecheck logs, and scan records.
• artifacts/search/leanexplore/ stores optional LeanExplore declaration-search records when the user explicitly chooses that manual MCP workflow.
• artifacts/remote/axle/ stores optional AXLE remote-result records when the user explicitly chooses that manual MCP workflow.
• README.md summarizes the local policy.

A Lean artifact may support a final report claim only after the parent has recorded typecheck evidence, placeholder/trust-base scan evidence, an accepted statement-equivalence review, and a lead or human review. Fake transports, stubs, sorry, admit, unsafe trust-base growth, or missing statement review cannot promote support.

AXLE MCP output, when present, is recorded as axle_remote_check evidence. It is supplemental context only: it cannot replace local formal_check evidence, set local Lean typecheck status, satisfy placeholder/trust-base scans, or promote formal support on its own.

LeanExplore MCP output, when present, is recorded as lean_declaration_search evidence. It is supplemental retrieval context only: it can help locate declarations, modules, source links, dependencies, and informalizations before drafting Lean, but it cannot replace local formal_check evidence or promote formal support on its own.

Use the local helpers as optional gates:

bash "$AAS_RUNTIME_ROOT/run_skill.sh" \
  skills/lean-formalization-intake/run_lean_formalization_intake.sh assess --claim-id C1 --claim "..."

bash "$AAS_RUNTIME_ROOT/run_skill.sh" \
  skills/lean-strict-verification-gate/run_lean_strict_verification_gate.sh verify --input formal/artifacts/C1.lean --artifact-stage final_candidate --typecheck

These helpers do not install Lean, Lake, Mathlib, MCP servers, AXLE adapters, LeanExplore packages, local search data, or provider tooling. They report local availability and fail closed when a required tool is unavailable.

Optional post-analysis figure handoff

Only do this when the user explicitly asks for a figure or the report would materially benefit from one.

This handoff happens after analysis, not instead of analysis.

Produce a figure-brief.json with:

• figure_id
• title
• purpose
• source_ids
• diagram_family
• content_requirements
• layout_constraints
• output_dir

Use tikz-draw after the brief exists.

Keep:

• figure_id as F1, F2, ...
• source_ids tied to the supporting S* records from earlier phases
• output artifacts under a dedicated figures/ directory inside the research workspace when practical

Phase 3 — Write

Inputs:

• the analyzed theme matrix

• preserved source ids and uncertainty notes

• prior posts, templates, style guides, venue instructions, source ledgers, or supplied examples when the deliverable must match an existing format or voice

• the active writing-style profile and overlays selected from writing-style-settings.md and any domain overlay

• produce a structured output

• include only citations that survive from earlier phases

• inspect and follow relevant prior-format/style artifacts before drafting blog posts, articles, reports, or other publication-style prose; if they are absent, state that assumption instead of inventing a house style

• distinguish observation, inference, and recommendation

• say incomplete analysis if material scope remains unchecked

Outputs:

• a final report
• a scoped source list
• optional delivery.json decision record
• optional writing_style.json or embedded writing_style_record with style_profile_ref and style_applied
• optional F* figure references with artifact paths
• explicit follow-up items when needed

Output structure guidance:

• references/output-structure.md
• references/research-quality-guards.md
• installed template deep-research-report

Skill handoffs

• Use docling before or between Phases 1 and 2 when local PDFs, HTML exports, or office documents need structure-aware parsing.
• Use database-lookup during Phase 1 when the task depends on structured public database records rather than general web synthesis.
• Use paper-lookup during Phase 1 when external literature metadata/discovery is needed after the local library-first workflow.
• Use research-digest-wrapper or rss-news-digest to seed Phase 1 when the task starts from tracked topics, alerts, or feeds.
• Use tikz-draw only after Phase 2 when there is an explicit figure request or a clear post-analysis figure brief to execute.
• Use formal-skeleton-helper, lean-formalization-intake, lean-explore-mcp, and lean-strict-verification-gate only for optional formalization candidates; they supplement the research workflow and do not replace source, computation, or human mathematical review.
• Use lean-explore-mcp only for manual optional Lean declaration search setup. Treat its results as lean_declaration_search evidence, not as local formal proof evidence.
• Use axiom-axle-mcp only for manual optional AXLE MCP setup. Treat its results as axle_remote_check evidence, not as local formal proof evidence.

Escalation rules

• Stay in this skill for single-agent phased deep research.
• Escalate to prose when the user explicitly wants structured multi-agent research-and-synthesis orchestration.
• Escalate to agent-group-discuss when the user wants panel-style discussion, debate, or multi-agent research perspectives.

Guardrails

• Do not invent sources.
• Do not collapse citations into vague "various sources" language.
• Keep the workflow provider-agnostic.
• Use narrower skills first when the task is really paper retrieval, database lookup, or simple browsing.
• If a task is document-heavy, parse first with docling rather than pretending plain-text extraction is equivalent.
• Do not drop a Phase 1 source silently in later phases; if it is excluded, note why.
• Do not reuse one source id for multiple different sources.
• Do not skip the Zotero cross-check for paper-like sources.
• Do not collapse research and drafting into one step when the user asks for a new post, article, report, or format-matched deliverable; inspect relevant prior context first, then write from the analyzed evidence.

Verification

• Phase 1 search results are explicitly recorded with stable S* ids
• Paper-like sources have Zotero verification status
• Important claims retain source linkage through Phase 3
• Optional figure briefs preserve S* source linkage and assign stable F* ids
• Final output distinguishes sourced fact from inference
• Missing coverage is disclosed explicitly
• Prior posts, templates, style guides, or supplied examples were inspected before format-matched writing, or their absence was disclosed
• writing-style-settings.md was loaded before final writing
• Mathematical or LaTeX output loaded math-manuscript-style.md
• Finalizable writing records style_profile_ref, active_overlays, active_requirement_ids, and style_applied
• Dropped or excluded sources are explained
• Nontrivial runs include guard outputs with guard_output_id
• Supported pass or warn guard outputs cite source or evidence IDs
• V2 claims cite evidence IDs, not only source IDs
• Formalized claims have formal_targets.jsonl, statement_equivalence_reviews.jsonl, scan/typecheck artifacts, and lead or human review before support is promoted
• LeanExplore declaration searches, if used, are recorded as supplemental lean_declaration_search evidence and do not replace local formal_check evidence
• AXLE remote checks, if used, are recorded as supplemental axle_remote_check evidence and paired with local formal_check evidence before any formal support is promoted
• Budget/model policy state is recorded only in parent-owned runbook artifacts
• No aggregate research quality score replaces guard outputs

Sample prompt shapes

• "Do a deep research workflow on X and preserve citations across phases."
• "Research X in three phases: search, analysis, and final report."