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.
Installation
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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:
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:
search
analyze
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.
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.
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
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."
