Indication dossier

Five research phases, each writing one waypoint JSON under <workdir>/waypoints/, ending in a cited Markdown report. Waypoints make the run resumable: a later invocation reads which files exist and continues from the first missing one. The only pause for user input is after Phase 1.

The framing rule

Treat the indication as a patient population, not a disease entry. Every section answers a population question — who are these patients, how are they identified and managed, which trials would help them — rather than a textbook question about the condition. Nesting is population nesting: everyone in the child indication is in the parent.

Some inputs are not billable diagnoses at all: a biological state ("immunosenescence"), a non-accepted indication ("ageing"), an iatrogenic population ("GLP-1 induced sarcopenia"). Detect and label this early — it changes the epidemiology evidence base, the regulatory path, and what a "complete" dossier even looks like.

Inputs

Input	Required	Meaning
indication	yes	e.g. "sarcopenia", "idiopathic pulmonary fibrosis"
additional_context	no	focus areas, parent indication, framing
workdir	no	waypoint/report location; default ./do_not_commit/indication-dossier-<slug>/

Tooling

Preferred: clinical-trials MCP for CT.gov, pubmed MCP for literature, WebSearch/WebFetch for FDA guidance, specialty-society guidelines (NCCN, AASLD, …), and CDC/WHO data; WebFetch for remote PDFs, Read for local ones; Agent subagents for parallel evidence gathering. When a listed MCP is not connected, say so and fall back to WebSearch against the public site itself.

Run protocol

Read references/standards.md first — it defines what counts as a citable finding, the anti-fabrication rules, and the report style. Phase-by-phase instructions live in references/phases.md; waypoint formats in references/waypoints.md.

1. Identity. Resolve definition, ICD codes, aliases, parent, diagnostic status; quick CT.gov landscape count. Write meta.json. Then show the resolved identity and end the turn asking Proceed / Revise identity / Stop — the expensive phases wait for the answer (Wisp has no separate interactive-question tool, so this is a normal turn end).
2. Epidemiology. Case definition, prevalence/incidence, demographics, natural history → epidemiology.json.
3. Biology & standard of care. Mechanism, biomarkers, approved therapies, guidelines, unmet need → biology_soc.json.
4. Regulatory & trials. Accepted endpoints, precedents, design parameters, landmark trials, failures → regulatory_trials.json.
5. Synthesis. No new research threads (single targeted gap-fills only). Write indication_dossier_report.md and research_output.json, then mark progress.json complete.

After each of phases 2–5, write the waypoint, emit a ≤200-word summary of findings and open uncertainties, and continue directly.

Resuming

When workdir already contains waypoints: list which phases are complete (file exists and is non-empty), show the meta summary, and ask which phase to run. Never overwrite an existing waypoint without confirmation.

Output layout

<workdir>/waypoints/
├── progress.json                 # loop control, flipped last
├── meta.json                     # phase 1
├── epidemiology.json             # phase 2
├── biology_soc.json              # phase 3
├── regulatory_trials.json        # phase 4
├── sources_evaluated.json        # appended by every phase
├── research_output.json          # phase 5, structured
└── indication_dossier_report.md  # phase 5, the deliverable