heor-agent-mcp 0.1.0 → 0.1.2

package/README.md

@@ -1,10 +1,30 @@
 # HEORAgent MCP Server
 
-An AI-powered Health Economics and Outcomes Research (HEOR) agent for Claude.ai — automates literature review, cost-effectiveness modelling, and HTA dossier preparation.
+[![npm version](https://img.shields.io/npm/v/heor-agent-mcp.svg)](https://www.npmjs.com/package/heor-agent-mcp)
+[![license](https://img.shields.io/npm/l/heor-agent-mcp.svg)](./LICENSE)
+[![node](https://img.shields.io/node/v/heor-agent-mcp.svg)](https://nodejs.org)
+
+**AI-powered Health Economics and Outcomes Research (HEOR) agent as a Model Context Protocol server.**
+
+Automates literature review across 41 data sources, state-of-the-art cost-effectiveness modelling, HTA dossier preparation for NICE / EMA / FDA / IQWiG / HAS / EU JCA, and a persistent project knowledge base — all callable as MCP tools from Claude.ai, Claude Code, and any MCP-compatible host.
+
+Built for pharmaceutical, biotech, CRO, and medical affairs teams who need rigorous, auditable HEOR workflows without building infrastructure from scratch.
+
+---
 
 ## Quick Start
 
-Add to your Claude.ai MCP configuration:
+### Claude Code
+
+```bash
+claude mcp add heor-agent -- npx heor-agent-mcp
+```
+
+Then restart Claude Code.
+
+### Claude Desktop / claude.ai
+
+Add to your MCP configuration:
 
 ```json
 {
@@ -17,136 +37,287 @@ Add to your Claude.ai MCP configuration:
 }
 ```
 
-Or run locally:
+### Verify
 
-```bash
-npm install heor-agent-mcp
-npx heor-agent-mcp
+```
+> Run a literature search for semaglutide cost-effectiveness in T2D using PubMed and NICE TAs
 ```
 
-## Tools
+---
 
-### literature_search
+## Tools
 
-Search PubMed, ClinicalTrials.gov, bioRxiv/medRxiv, and ChEMBL simultaneously.
-Returns structured results with a full PRISMA-style audit trail.
+| Tool | Purpose |
+|------|---------|
+| `literature_search` | Search 41 data sources with a full PRISMA-style audit trail |
+| `cost_effectiveness_model` | Markov / PartSA / decision-tree CEA with PSA, OWSA, CEAC, EVPI |
+| `hta_dossier_prep` | Draft submissions for NICE, EMA, FDA, IQWiG, HAS, and EU JCA |
+| `project_create` | Initialize a persistent project workspace |
+| `knowledge_search` | Full-text search across a project's raw/ and wiki/ trees |
+| `knowledge_read` | Read any file from a project's knowledge base |
+| `knowledge_write` | Write compiled evidence to the project wiki (Obsidian-compatible) |
 
-**Required**: `query` (string)  
-**Optional**: `sources` (array), `max_results` (1–100), `date_from` (YYYY-MM-DD), `output_format` (text|json|docx)
+### `literature_search`
 
-**Example prompt**: "Find RCT evidence on semaglutide for type 2 diabetes from the last 3 years"
+Searches across 41 sources in parallel. Every call returns a **source selection table** showing which of the 41 sources were used and why — essential for HTA audit trails.
 
-### cost_effectiveness_model
+**Example call:**
+```json
+{
+  "query": "semaglutide cardiovascular outcomes type 2 diabetes",
+  "sources": ["pubmed", "clinicaltrials", "nice_ta", "cadth_reviews", "icer_reports"],
+  "max_results": 20,
+  "output_format": "text"
+}
+```
 
-State-of-the-art cost-utility analysis: multi-state Markov model, probabilistic sensitivity
-analysis (PSA, Monte Carlo), one-way sensitivity analysis (tornado diagram), cost-effectiveness
-acceptability curve (CEAC), and Expected Value of Perfect Information (EVPI).
+### `cost_effectiveness_model`
 
-Follows ISPOR good practice guidelines and NICE reference case (3.5% discount rate).
+Multi-state Markov model (default) or Partitioned Survival Analysis (oncology), following ISPOR good practice and NICE reference case (3.5% discount rate, half-cycle correction). Includes:
 
-**Required**: `intervention`, `comparator`, `indication`, `time_horizon`, `perspective`, `clinical_inputs`, `cost_inputs`  
-**Optional**: `model_type` (markov|partsa|decision_tree), `utility_inputs`, `run_psa`, `psa_iterations`, `run_owsa`
+- **PSA** — 1,000–10,000 Monte Carlo iterations, probability cost-effective at WTP thresholds
+- **OWSA** — one-way sensitivity analysis with tornado summary
+- **CEAC** — cost-effectiveness acceptability curve
+- **EVPI** — expected value of perfect information
+- **WTP assessment** — verdict against NHS (£20–30K), US payer ($100–150K), societal thresholds
 
-**Supported HTA perspectives**:
-- `nhs` — NICE threshold £20–30K/QALY
-- `us_payer` — ICER threshold $100–150K/QALY
-- `societal` — Societal perspective $50–100K/QALY
+**Example call:**
+```json
+{
+  "intervention": "Semaglutide 1mg SC weekly",
+  "comparator": "Sitagliptin 100mg daily",
+  "indication": "Type 2 Diabetes Mellitus",
+  "time_horizon": "lifetime",
+  "perspective": "nhs",
+  "model_type": "markov",
+  "clinical_inputs": { "efficacy_delta": 0.5, "mortality_reduction": 0.15 },
+  "cost_inputs": { "drug_cost_annual": 3200, "comparator_cost_annual": 480 },
+  "utility_inputs": { "qaly_on_treatment": 0.82, "qaly_comparator": 0.76 },
+  "run_psa": true,
+  "output_format": "docx"
+}
+```
 
-For oncology: set `model_type="partsa"` to use Partitioned Survival Analysis (NICE TSD 14).
+### `hta_dossier_prep`
 
-**Example prompt**: "Model cost-effectiveness of semaglutide vs sitagliptin for T2D, NHS perspective, lifetime horizon"
+Drafts submission-ready sections for six HTA frameworks with gap analysis:
 
-### hta_dossier_prep
+| Body | Country | Submission types |
+|------|---------|------------------|
+| NICE | UK | STA, MTA, early_access |
+| EMA | EU | STA, MTA |
+| FDA | US | STA, MTA |
+| IQWiG | Germany | STA, MTA |
+| HAS | France | STA, MTA |
+| JCA | EU (Reg. 2021/2282) | initial, renewal, variation (with PICOs) |
 
-Structure evidence into submission-ready HTA dossier sections with gap analysis.
-Accepts output from `literature_search` and `cost_effectiveness_model` directly.
+Accepts piped output from `literature_search` and `cost_effectiveness_model`.
 
-**Required**: `hta_body` (nice|ema|fda|iqwig|has), `submission_type` (sta|mta|early_access), `drug_name`, `indication`  
-**Optional**: `evidence_summary` (text or JSON from literature_search), `model_results` (from cost_effectiveness_model)
+### Knowledge base tools
 
-**Supported bodies**: NICE (UK), EMA (EU), FDA (US), IQWiG (Germany), HAS (France)
+Projects live at `~/.heor-agent/projects/{project-id}/` with:
+- `raw/literature/` — auto-populated literature search results
+- `raw/models/` — auto-populated model runs
+- `raw/dossiers/` — auto-populated dossier drafts
+- `reports/` — generated DOCX files
+- `wiki/` — manually curated, Obsidian-compatible markdown with `[[wikilinks]]`
 
-**Example prompt**: "Prepare a NICE STA outline for semaglutide in type 2 diabetes using [literature search output]"
+Pass `project: "project-id"` to any tool and results are saved automatically.
 
-## Audit Trail
+---
 
-Every tool call returns a full audit record:
-- Sources queried, queries sent, response counts
-- Inclusion/exclusion counts with reasons
-- Methodology notes and assumptions
-- Warnings and data quality flags
+## Data Sources
 
-Suitable for inclusion in HTA submission appendices.
+**41 sources across 9 categories.** Every `literature_search` call includes a source selection table showing used/not-used status and reason for each.
 
-## Data Sources (Phase 1 — DirectProvider)
+<details>
+<summary><b>Biomedical & Clinical Trials (4)</b></summary>
 
-Currently integrated (free, direct API access):
 - **PubMed** — 35M+ biomedical citations (NCBI E-utilities)
-- **ClinicalTrials.gov** — FDA-regulated clinical studies (CT.gov v2 API)
+- **ClinicalTrials.gov** — NIH/NLM trial registry (CT.gov v2 API)
 - **bioRxiv / medRxiv** — Life sciences and medical preprints
 - **ChEMBL** — Drug bioactivity, mechanisms, ADMET (EMBL-EBI)
+</details>
+
+<details>
+<summary><b>Epidemiology & Demographics (5)</b></summary>
+
+- **WHO GHO** — WHO Global Health Observatory
+- **World Bank** — Demographics, macroeconomics, health expenditure
+- **OECD Health** — OECD health statistics (expenditure, workforce, outcomes)
+- **IHME GBD** — Global Burden of Disease (DALYs, prevalence across 204 countries)
+- **All of Us** — NIH precision medicine cohort
+</details>
+
+<details>
+<summary><b>FDA (2)</b></summary>
+
+- **FDA Orange Book** — Drug approvals and therapeutic equivalence
+- **FDA Purple Book** — Licensed biologics and biosimilars
+</details>
+
+<details>
+<summary><b>HTA Appraisals (10) — HTA precedent decisions</b></summary>
+
+- **NICE TAs** (UK) · **CADTH** (Canada) · **ICER** (US) · **PBAC** (Australia)
+- **G-BA AMNOG** (Germany) · **IQWiG** (Germany) · **HAS** (France)
+- **AIFA** (Italy) · **TLV** (Sweden) · **INESSS** (Quebec, Canada)
+</details>
+
+<details>
+<summary><b>HTA Cost References (5)</b></summary>
+
+- **CMS NADAC** (US drug acquisition costs)
+- **PSSRU** (UK unit costs) · **NHS National Cost Collection** · **BNF** (UK drug pricing)
+- **PBS Schedule** (Australia)
+</details>
+
+<details>
+<summary><b>LATAM (6)</b></summary>
 
-## Data Sources (Roadmap)
-
-### Phase 2 — Open/Free APIs
-- WHO Global Health Observatory — Global epidemiology and health indicators
-- World Bank Data — Demographics, macroeconomics
-- OECD Health Data — Costs, utilization, health statistics (OECD)
-- IHME / Global Burden of Disease — Global disease burden estimates
-- ISPOR Presentations Database — HEOR studies and conference posters
-
-### Phase 2 — HTA Guidance & Pricing (Open)
-- NICE (UK): Methods Guide, Technology Appraisals, PSSRU Unit Costs, NHS Reference Costs, BNF
-- ICER (US): Value Assessment Framework, CMS Data
-- CADTH (Canada): Guidelines and Reviews, INESSS
-- PBAC (Australia): Guidelines, PSD, PBS/MBS Schedule
-- HAS (France): Guidelines, Transparency Committee, CEPS
-- IQWiG/G-BA (Germany): Methods Guide, Appraisal Decisions
-- AIFA (Italy), AEMPS/IPT (Spain), TLV (Sweden), MHLW (Japan)
-- CONITEC/ANVISA (Brazil), IETS (Colombia), FONASA (Chile), HITAP (Thailand)
-- HIRA/NHIS (South Korea), WHO GHO, OECD Health, World Bank
-
-### Phase 2 — Restricted (with credentials)
-- CPRD (UK primary care), NHS HES (UK hospital episodes), SNDS (France national claims)
-- German SHI/AOK/WIdO, Nordic Registries, Japan NDB, NHIRD (Taiwan)
-- NHSO (Thailand), PhilHealth (Philippines)
-
-### Phase 3 — Commercial (enterprise tier)
-- IQVIA MIDAS/RWD, Optum Clinformatics, Flatiron Health (oncology EHR)
-- Premier Healthcare Database, Komodo Health, Oracle Health RWD
-- IBM Micromedex Red Book (drug pricing), SSR Health (net pricing/rebates)
-
-## Local RWE Datasets (Phase 2)
-
-Point to local files in `/Users/mnaumov/Projects/Health_Statistics`:
-- NAMCS — National Ambulatory Medical Care Survey (US)
-- NHAMCS — National Hospital Ambulatory Medical Care Survey (US)
-- MEPS — Medical Expenditure Panel Survey (US)
-- DATASUS — Brazilian health system data (hospital + epidemiology)
-
-## Tiers
-
-- **DirectProvider** (default) — Free. Uses your Anthropic API key. All tools, text + JSON output.
-- **HostedProvider** — Set `HEOR_API_KEY` env var. Phase 2: DOCX/PDF reports, Redis caching.
+- **DATASUS** · **CONITEC** · **ANVISA** (Brazil)
+- **PAHO** (Pan American regional) · **IETS** (Colombia) · **FONASA** (Chile)
+</details>
+
+<details>
+<summary><b>APAC (1)</b></summary>
+
+- **HITAP** (Thailand)
+</details>
+
+<details>
+<summary><b>Enterprise (6) — require API key</b></summary>
+
+| Source | Env variable |
+|--------|--------------|
+| Embase | `ELSEVIER_API_KEY` |
+| ScienceDirect | `ELSEVIER_API_KEY` |
+| Cochrane Library | `COCHRANE_API_KEY` |
+| Citeline | `CITELINE_API_KEY` |
+| Pharmapendium | `PHARMAPENDIUM_API_KEY` |
+| Cortellis | `CORTELLIS_API_KEY` |
+| Google Scholar | `SERPAPI_KEY` |
+</details>
+
+<details>
+<summary><b>Other (1)</b></summary>
+
+- **ISPOR** — HEOR methodology and conference abstracts
+</details>
+
+---
+
+## Output Formats
+
+All tools support `output_format`:
+
+- **`text`** (default) — Markdown with formatted tables and headings
+- **`json`** — Structured objects for downstream tools
+- **`docx`** — Microsoft Word document, saved to disk, path returned in response
+
+DOCX files are saved to `~/.heor-agent/projects/{project}/reports/` (when a project is set) or `~/.heor-agent/reports/` (global). The tool response contains the absolute path — ready to attach to submissions or share with stakeholders.
+
+---
+
+## Audit Trail
+
+Every tool call returns a full audit record:
+
+- **Source selection table** — all 41 sources with used/not-used and reason
+- **Sources queried** — queries sent, response counts, status, latency
+- **Inclusions / exclusions** — counts with reasons
+- **Methodology** — PRISMA-style for literature, ISPOR/NICE for economics
+- **Assumptions** — every assumption logged with justification
+- **Warnings** — data quality flags, missing API keys, failed sources
+
+Suitable for inclusion in HTA submission appendices.
+
+---
 
 ## Configuration
 
 ```bash
-HEOR_API_KEY   # Set to enable HostedProvider (Phase 2). Omit for DirectProvider (Phase 1).
+# Optional — enterprise data sources
+ELSEVIER_API_KEY=...        # Embase + ScienceDirect
+COCHRANE_API_KEY=...        # Cochrane Library
+CITELINE_API_KEY=...        # Citeline
+PHARMAPENDIUM_API_KEY=...   # Pharmapendium
+CORTELLIS_API_KEY=...       # Cortellis
+SERPAPI_KEY=...             # Google Scholar
+
+# Optional — knowledge base location
+HEOR_KB_ROOT=~/.heor-agent  # Default
+
+# Optional — localhost proxy for enterprise APIs behind corporate VPN
+HEOR_PROXY_URL=http://localhost:8787
+
+# Optional — hosted tier (future)
+HEOR_API_KEY=...
 ```
 
+---
+
 ## Development
 
 ```bash
+git clone https://github.com/neptun2000/HEORAgent
+cd HEORAgent/heor-agent-mcp
 npm install
-npm test          # 74 tests
-npm run build     # Compiles to dist/
+npm test          # 244 tests across 66 suites
+npm run build     # Compile TypeScript to dist/
 npm run dev       # Run with tsx (no build step)
 ```
 
-Node.js >= 20 required.
+**Requires:** Node.js ≥ 20.
+
+---
+
+## Architecture
+
+```
+┌────────────────────────────────────────────┐
+│  MCP Host (Claude.ai / Claude Code / etc.) │
+└────────────────┬───────────────────────────┘
+                 │ stdio
+┌────────────────▼──────────────────────────┐
+│  heor-agent-mcp server                    │
+│  ┌──────────────────────────────────────┐ │
+│  │ 7 MCP tools (Zod-validated)          │ │
+│  ├──────────────────────────────────────┤ │
+│  │ DirectProvider (default)             │ │
+│  │   ├─ 41 source fetchers              │ │
+│  │   ├─ Audit builder + PRISMA trail    │ │
+│  │   ├─ Markov / PartSA economic models │ │
+│  │   ├─ Markdown + DOCX formatters      │ │
+│  │   └─ Knowledge base (YAML + MD)      │ │
+│  └──────────────────────────────────────┘ │
+└───────────────────────────────────────────┘
+                 │
+    ┌────────────┴─────────────┐
+    ▼                          ▼
+┌────────────┐         ┌──────────────────┐
+│ ~/.heor-   │         │ External APIs    │
+│ agent/     │         │ (PubMed, NICE,   │
+│ projects/  │         │  ICER, CADTH, …) │
+└────────────┘         └──────────────────┘
+```
+
+---
+
+## License
+
+MIT — see [LICENSE](./LICENSE).
+
+---
 
 ## Disclaimer
 
-All outputs are preliminary and for research orientation only. Results require validation by a
-qualified health economist before use in any HTA submission, payer negotiation, or clinical decision.
+**All outputs are preliminary and for research orientation only.** Results require validation by a qualified health economist before use in any HTA submission, payer negotiation, regulatory filing, or clinical decision. This tool does not replace professional HEOR expertise.
+
+---
+
+## Links
+
+- **npm:** https://www.npmjs.com/package/heor-agent-mcp
+- **GitHub:** https://github.com/neptun2000/HEORAgent
+- **Issues:** https://github.com/neptun2000/HEORAgent/issues

package/dist/audit/types.d.ts

@@ -12,12 +12,21 @@ export interface ExclusionRecord {
     title: string;
     reason: string;
 }
+export interface SourceSelectionRow {
+    source: string;
+    name: string;
+    category: string;
+    used: boolean;
+    reason: string;
+}
 export interface AuditRecord {
     tool: string;
     /** ISO 8601 timestamp when the tool invocation began (query start time, not completion time) */
     timestamp: string;
     query: Record<string, unknown>;
     sources_queried: SourceAudit[];
+    /** Full source selection table showing all available sources with used/not-used and reason */
+    source_selection?: SourceSelectionRow[];
     methodology: string;
     /** Running total of results included across all sources — incremented by addSource() */
     inclusions: number;

package/dist/audit/types.d.ts.map

@@ -1 +1 @@
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package/dist/formatters/markdown.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"markdown.d.ts","sourceRoot":"","sources":["../../src/formatters/markdown.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,uBAAuB,CAAC;AAC9D,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,mBAAmB,CAAC;AAErD,wBAAgB,iBAAiB,CAC/B,OAAO,EAAE,gBAAgB,EAAE,EAC3B,KAAK,EAAE,WAAW,GACjB,MAAM,CA4BR;AAED,wBAAgB,eAAe,CAAC,KAAK,EAAE,WAAW,GAAG,MAAM,CAiD1D"}

package/dist/formatters/markdown.js

@@ -25,6 +25,14 @@ export function auditToMarkdown(audit) {
     lines.push(`## Audit Report`);
     lines.push(`**Tool:** ${audit.tool} | **Time:** ${audit.timestamp} | **Methodology:** ${audit.methodology || "N/A"}`);
     lines.push(`**Total included:** ${audit.inclusions}`);
+    if (audit.source_selection && audit.source_selection.length > 0) {
+        lines.push(`\n### Source Selection (${audit.source_selection.filter((s) => s.used).length}/${audit.source_selection.length} sources used)`);
+        lines.push(`| Source | Category | Used | Reason |`);
+        lines.push(`|--------|----------|------|--------|`);
+        audit.source_selection.forEach((s) => {
+            lines.push(`| ${s.name} | ${s.category} | ${s.used ? "YES" : "NO"} | ${s.reason} |`);
+        });
+    }
     if (audit.sources_queried.length > 0) {
         lines.push(`\n### Sources Queried`);
         lines.push(`| Source | Query | Returned | Included | Status |`);

package/dist/formatters/markdown.js.map

@@ -1 +1 @@
-{"version":3,"file":"markdown.js","sourceRoot":"","sources":["../../src/formatters/markdown.ts"],"names":[],"mappings":"AAGA,MAAM,UAAU,iBAAiB,CAC/B,OAA2B,EAC3B,KAAkB;IAElB,MAAM,KAAK,GAAa,EAAE,CAAC;IAE3B,KAAK,CAAC,IAAI,CAAC,8BAA8B,CAAC,CAAC;IAC3C,KAAK,CAAC,IAAI,CACR,IAAI,OAAO,CAAC,MAAM,4BAA4B,KAAK,CAAC,eAAe,CAAC,MAAM,aAAa,CACxF,CAAC;IAEF,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACzB,KAAK,CAAC,IAAI,CAAC,uCAAuC,CAAC,CAAC;IACtD,CAAC;SAAM,CAAC;QACN,OAAO,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE;YACvB,KAAK,CAAC,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC;YACvC,KAAK,CAAC,IAAI,CACR,eAAe,CAAC,CAAC,MAAM,gBAAgB,CAAC,CAAC,IAAI,gBAAgB,CAAC,CAAC,UAAU,EAAE,CAC5E,CAAC;YACF,IAAI,CAAC,CAAC,OAAO,CAAC,MAAM,GAAG,CAAC;gBACtB,KAAK,CAAC,IAAI,CAAC,gBAAgB,CAAC,CAAC,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;YACrD,IAAI,CAAC,CAAC,QAAQ;gBACZ,KAAK,CAAC,IAAI,CACR,KAAK,CAAC,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC,EAAE,GAAG,CAAC,GAAG,CAAC,CAAC,QAAQ,CAAC,MAAM,GAAG,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,EAAE,CACvE,CAAC;YACJ,KAAK,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC;QACpC,CAAC,CAAC,CAAC;IACL,CAAC;IAED,KAAK,CAAC,IAAI,CAAC,eAAe,CAAC,KAAK,CAAC,CAAC,CAAC;IACnC,OAAO,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;AAC1B,CAAC;AAED,MAAM,UAAU,eAAe,CAAC,KAAkB;IAChD,MAAM,KAAK,GAAa,EAAE,CAAC;IAC3B,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;IAClB,KAAK,CAAC,IAAI,CAAC,iBAAiB,CAAC,CAAC;IAC9B,KAAK,CAAC,IAAI,CACR,aAAa,KAAK,CAAC,IAAI,gBAAgB,KAAK,CAAC,SAAS,uBAAuB,KAAK,CAAC,WAAW,IAAI,KAAK,EAAE,CAC1G,CAAC;IACF,KAAK,CAAC,IAAI,CAAC,uBAAuB,KAAK,CAAC,UAAU,EAAE,CAAC,CAAC;IAEtD,IAAI,KAAK,CAAC,eAAe,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACrC,KAAK,CAAC,IAAI,CAAC,uBAAuB,CAAC,CAAC;QACpC,KAAK,CAAC,IAAI,CAAC,mDAAmD,CAAC,CAAC;QAChE,KAAK,CAAC,IAAI,CAAC,mDAAmD,CAAC,CAAC;QAChE,KAAK,CAAC,eAAe,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,EAAE;YAClC,KAAK,CAAC,IAAI,CACR,KAAK,CAAC,CAAC,MAAM,QAAQ,CAAC,CAAC,UAAU,QAAQ,CAAC,CAAC,gBAAgB,MAAM,CAAC,CAAC,gBAAgB,MAAM,CAAC,CAAC,MAAM,IAAI,CACtG,CAAC;QACJ,CAAC,CAAC,CAAC;IACL,CAAC;IAED,IAAI,KAAK,CAAC,UAAU,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QAChC,KAAK,CAAC,IAAI,CAAC,qBAAqB,KAAK,CAAC,UAAU,CAAC,MAAM,GAAG,CAAC,CAAC;QAC5D,KAAK,CAAC,UAAU,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,KAAK,MAAM,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC;IAC7E,CAAC;IAED,IAAI,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACjC,KAAK,CAAC,IAAI,CAAC,mBAAmB,CAAC,CAAC;QAChC,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC,CAAC;IACzD,CAAC;IAED,IAAI,KAAK,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QAC9B,KAAK,CAAC,IAAI,CAAC,gBAAgB,CAAC,CAAC;QAC7B,KAAK,CAAC,QAAQ,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAC,CAAC;IACzD,CAAC;IAED,OAAO,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;AAC1B,CAAC"}
+{"version":3,"file":"markdown.js","sourceRoot":"","sources":["../../src/formatters/markdown.ts"],"names":[],"mappings":"AAGA,MAAM,UAAU,iBAAiB,CAC/B,OAA2B,EAC3B,KAAkB;IAElB,MAAM,KAAK,GAAa,EAAE,CAAC;IAE3B,KAAK,CAAC,IAAI,CAAC,8BAA8B,CAAC,CAAC;IAC3C,KAAK,CAAC,IAAI,CACR,IAAI,OAAO,CAAC,MAAM,4BAA4B,KAAK,CAAC,eAAe,CAAC,MAAM,aAAa,CACxF,CAAC;IAEF,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACzB,KAAK,CAAC,IAAI,CAAC,uCAAuC,CAAC,CAAC;IACtD,CAAC;SAAM,CAAC;QACN,OAAO,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE;YACvB,KAAK,CAAC,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC;YACvC,KAAK,CAAC,IAAI,CACR,eAAe,CAAC,CAAC,MAAM,gBAAgB,CAAC,CAAC,IAAI,gBAAgB,CAAC,CAAC,UAAU,EAAE,CAC5E,CAAC;YACF,IAAI,CAAC,CAAC,OAAO,CAAC,MAAM,GAAG,CAAC;gBACtB,KAAK,CAAC,IAAI,CAAC,gBAAgB,CAAC,CAAC,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;YACrD,IAAI,CAAC,CAAC,QAAQ;gBACZ,KAAK,CAAC,IAAI,CACR,KAAK,CAAC,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC,EAAE,GAAG,CAAC,GAAG,CAAC,CAAC,QAAQ,CAAC,MAAM,GAAG,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,EAAE,CACvE,CAAC;YACJ,KAAK,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC;QACpC,CAAC,CAAC,CAAC;IACL,CAAC;IAED,KAAK,CAAC,IAAI,CAAC,eAAe,CAAC,KAAK,CAAC,CAAC,CAAC;IACnC,OAAO,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;AAC1B,CAAC;AAED,MAAM,UAAU,eAAe,CAAC,KAAkB;IAChD,MAAM,KAAK,GAAa,EAAE,CAAC;IAC3B,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;IAClB,KAAK,CAAC,IAAI,CAAC,iBAAiB,CAAC,CAAC;IAC9B,KAAK,CAAC,IAAI,CACR,aAAa,KAAK,CAAC,IAAI,gBAAgB,KAAK,CAAC,SAAS,uBAAuB,KAAK,CAAC,WAAW,IAAI,KAAK,EAAE,CAC1G,CAAC;IACF,KAAK,CAAC,IAAI,CAAC,uBAAuB,KAAK,CAAC,UAAU,EAAE,CAAC,CAAC;IAEtD,IAAI,KAAK,CAAC,gBAAgB,IAAI,KAAK,CAAC,gBAAgB,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QAChE,KAAK,CAAC,IAAI,CACR,2BAA2B,KAAK,CAAC,gBAAgB,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,MAAM,gBAAgB,CAChI,CAAC;QACF,KAAK,CAAC,IAAI,CAAC,uCAAuC,CAAC,CAAC;QACpD,KAAK,CAAC,IAAI,CAAC,uCAAuC,CAAC,CAAC;QACpD,KAAK,CAAC,gBAAgB,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,EAAE;YACnC,KAAK,CAAC,IAAI,CACR,KAAK,CAAC,CAAC,IAAI,MAAM,CAAC,CAAC,QAAQ,MAAM,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,IAAI,MAAM,CAAC,CAAC,MAAM,IAAI,CACzE,CAAC;QACJ,CAAC,CAAC,CAAC;IACL,CAAC;IAED,IAAI,KAAK,CAAC,eAAe,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACrC,KAAK,CAAC,IAAI,CAAC,uBAAuB,CAAC,CAAC;QACpC,KAAK,CAAC,IAAI,CAAC,mDAAmD,CAAC,CAAC;QAChE,KAAK,CAAC,IAAI,CAAC,mDAAmD,CAAC,CAAC;QAChE,KAAK,CAAC,eAAe,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,EAAE;YAClC,KAAK,CAAC,IAAI,CACR,KAAK,CAAC,CAAC,MAAM,QAAQ,CAAC,CAAC,UAAU,QAAQ,CAAC,CAAC,gBAAgB,MAAM,CAAC,CAAC,gBAAgB,MAAM,CAAC,CAAC,MAAM,IAAI,CACtG,CAAC;QACJ,CAAC,CAAC,CAAC;IACL,CAAC;IAED,IAAI,KAAK,CAAC,UAAU,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QAChC,KAAK,CAAC,IAAI,CAAC,qBAAqB,KAAK,CAAC,UAAU,CAAC,MAAM,GAAG,CAAC,CAAC;QAC5D,KAAK,CAAC,UAAU,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,KAAK,MAAM,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC;IAC7E,CAAC;IAED,IAAI,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACjC,KAAK,CAAC,IAAI,CAAC,mBAAmB,CAAC,CAAC;QAChC,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC,CAAC;IACzD,CAAC;IAED,IAAI,KAAK,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QAC9B,KAAK,CAAC,IAAI,CAAC,gBAAgB,CAAC,CAAC;QAC7B,KAAK,CAAC,QAAQ,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAC,CAAC;IACzD,CAAC;IAED,OAAO,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;AAC1B,CAAC"}

package/dist/knowledge/index.d.ts

@@ -4,5 +4,6 @@ export * from "./rawStore.js";
 export * from "./search.js";
 export * from "./wikiStore.js";
 export * from "./projectStore.js";
+export * from "./reportStore.js";
 export * from "./types.js";
 //# sourceMappingURL=index.d.ts.map

package/dist/knowledge/index.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/knowledge/index.ts"],"names":[],"mappings":"AAAA,cAAc,YAAY,CAAC;AAC3B,cAAc,WAAW,CAAC;AAC1B,cAAc,eAAe,CAAC;AAC9B,cAAc,aAAa,CAAC;AAC5B,cAAc,gBAAgB,CAAC;AAC/B,cAAc,mBAAmB,CAAC;AAClC,cAAc,YAAY,CAAC"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/knowledge/index.ts"],"names":[],"mappings":"AAAA,cAAc,YAAY,CAAC;AAC3B,cAAc,WAAW,CAAC;AAC1B,cAAc,eAAe,CAAC;AAC9B,cAAc,aAAa,CAAC;AAC5B,cAAc,gBAAgB,CAAC;AAC/B,cAAc,mBAAmB,CAAC;AAClC,cAAc,kBAAkB,CAAC;AACjC,cAAc,YAAY,CAAC"}

package/dist/knowledge/index.js

@@ -4,5 +4,6 @@ export * from "./rawStore.js";
 export * from "./search.js";
 export * from "./wikiStore.js";
 export * from "./projectStore.js";
+export * from "./reportStore.js";
 export * from "./types.js";
 //# sourceMappingURL=index.js.map

package/dist/knowledge/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/knowledge/index.ts"],"names":[],"mappings":"AAAA,cAAc,YAAY,CAAC;AAC3B,cAAc,WAAW,CAAC;AAC1B,cAAc,eAAe,CAAC;AAC9B,cAAc,aAAa,CAAC;AAC5B,cAAc,gBAAgB,CAAC;AAC/B,cAAc,mBAAmB,CAAC;AAClC,cAAc,YAAY,CAAC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/knowledge/index.ts"],"names":[],"mappings":"AAAA,cAAc,YAAY,CAAC;AAC3B,cAAc,WAAW,CAAC;AAC1B,cAAc,eAAe,CAAC;AAC9B,cAAc,aAAa,CAAC;AAC5B,cAAc,gBAAgB,CAAC;AAC/B,cAAc,mBAAmB,CAAC;AAClC,cAAc,kBAAkB,CAAC;AACjC,cAAc,YAAY,CAAC"}

package/dist/knowledge/paths.d.ts

@@ -4,6 +4,7 @@ export declare function getRawLiteratureDir(projectId: string): string;
 export declare function getRawModelsDir(projectId: string): string;
 export declare function getRawDossiersDir(projectId: string): string;
 export declare function getWikiDir(projectId: string): string;
+export declare function getReportsDir(projectId?: string): string;
 export declare function sanitizeProjectId(id: string): string;
 export declare function sanitizeFilename(name: string): string;
 //# sourceMappingURL=paths.d.ts.map

package/dist/knowledge/paths.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"paths.d.ts","sourceRoot":"","sources":["../../src/knowledge/paths.ts"],"names":[],"mappings":"AAGA,wBAAgB,SAAS,IAAI,MAAM,CAElC;AAED,wBAAgB,cAAc,CAAC,SAAS,EAAE,MAAM,GAAG,MAAM,CAExD;AAED,wBAAgB,mBAAmB,CAAC,SAAS,EAAE,MAAM,GAAG,MAAM,CAE7D;AAED,wBAAgB,eAAe,CAAC,SAAS,EAAE,MAAM,GAAG,MAAM,CAEzD;AAED,wBAAgB,iBAAiB,CAAC,SAAS,EAAE,MAAM,GAAG,MAAM,CAE3D;AAED,wBAAgB,UAAU,CAAC,SAAS,EAAE,MAAM,GAAG,MAAM,CAEpD;AAGD,wBAAgB,iBAAiB,CAAC,EAAE,EAAE,MAAM,GAAG,MAAM,CAMpD;AAGD,wBAAgB,gBAAgB,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAErD"}
+{"version":3,"file":"paths.d.ts","sourceRoot":"","sources":["../../src/knowledge/paths.ts"],"names":[],"mappings":"AAGA,wBAAgB,SAAS,IAAI,MAAM,CAElC;AAED,wBAAgB,cAAc,CAAC,SAAS,EAAE,MAAM,GAAG,MAAM,CAExD;AAED,wBAAgB,mBAAmB,CAAC,SAAS,EAAE,MAAM,GAAG,MAAM,CAE7D;AAED,wBAAgB,eAAe,CAAC,SAAS,EAAE,MAAM,GAAG,MAAM,CAEzD;AAED,wBAAgB,iBAAiB,CAAC,SAAS,EAAE,MAAM,GAAG,MAAM,CAE3D;AAED,wBAAgB,UAAU,CAAC,SAAS,EAAE,MAAM,GAAG,MAAM,CAEpD;AAED,wBAAgB,aAAa,CAAC,SAAS,CAAC,EAAE,MAAM,GAAG,MAAM,CAKxD;AAGD,wBAAgB,iBAAiB,CAAC,EAAE,EAAE,MAAM,GAAG,MAAM,CAUpD;AAGD,wBAAgB,gBAAgB,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAErD"}

package/dist/knowledge/paths.js

@@ -18,10 +18,19 @@ export function getRawDossiersDir(projectId) {
 export function getWikiDir(projectId) {
     return join(getProjectRoot(projectId), "wiki");
 }
+export function getReportsDir(projectId) {
+    if (projectId) {
+        return join(getProjectRoot(projectId), "reports");
+    }
+    return join(getKbRoot(), "reports");
+}
 // Sanitize project ID to prevent path traversal and filesystem issues
 export function sanitizeProjectId(id) {
     // Allow alphanumeric, hyphens, underscores. Replace all else with hyphen.
-    const clean = id.replace(/[^a-zA-Z0-9_-]/g, "-").replace(/-+/g, "-").replace(/^-|-$/g, "");
+    const clean = id
+        .replace(/[^a-zA-Z0-9_-]/g, "-")
+        .replace(/-+/g, "-")
+        .replace(/^-|-$/g, "");
     if (clean.length === 0)
         throw new Error("Invalid project ID: must contain alphanumeric characters");
     if (clean.length > 64)

package/dist/knowledge/paths.js.map

@@ -1 +1 @@
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package/dist/knowledge/reportStore.d.ts

@@ -0,0 +1,10 @@
+/**
+ * Save a base64-encoded DOCX report to disk.
+ *
+ * If `projectId` is provided, saves to `~/.heor-agent/projects/{id}/reports/`.
+ * Otherwise saves to `~/.heor-agent/reports/`.
+ *
+ * @returns Absolute path to the saved file
+ */
+export declare function saveReport(base64: string, filenameStem: string, projectId?: string, extension?: string): Promise<string>;
+//# sourceMappingURL=reportStore.d.ts.map

package/dist/knowledge/reportStore.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"reportStore.d.ts","sourceRoot":"","sources":["../../src/knowledge/reportStore.ts"],"names":[],"mappings":"AAIA;;;;;;;GAOG;AACH,wBAAsB,UAAU,CAC9B,MAAM,EAAE,MAAM,EACd,YAAY,EAAE,MAAM,EACpB,SAAS,CAAC,EAAE,MAAM,EAClB,SAAS,GAAE,MAAe,GACzB,OAAO,CAAC,MAAM,CAAC,CAkBjB"}

package/dist/knowledge/reportStore.js

@@ -0,0 +1,27 @@
+import { mkdir, writeFile } from "node:fs/promises";
+import { join } from "node:path";
+import { getReportsDir, sanitizeFilename } from "./paths.js";
+/**
+ * Save a base64-encoded DOCX report to disk.
+ *
+ * If `projectId` is provided, saves to `~/.heor-agent/projects/{id}/reports/`.
+ * Otherwise saves to `~/.heor-agent/reports/`.
+ *
+ * @returns Absolute path to the saved file
+ */
+export async function saveReport(base64, filenameStem, projectId, extension = "docx") {
+    const dir = getReportsDir(projectId);
+    await mkdir(dir, { recursive: true });
+    const timestamp = new Date()
+        .toISOString()
+        .replace(/[:.]/g, "-")
+        .replace(/T/, "_")
+        .slice(0, 19);
+    const safeName = sanitizeFilename(filenameStem);
+    const filename = `${safeName}_${timestamp}.${extension}`;
+    const fullPath = join(dir, filename);
+    const buffer = Buffer.from(base64, "base64");
+    await writeFile(fullPath, buffer);
+    return fullPath;
+}
+//# sourceMappingURL=reportStore.js.map

package/dist/knowledge/reportStore.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"reportStore.js","sourceRoot":"","sources":["../../src/knowledge/reportStore.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,SAAS,EAAE,MAAM,kBAAkB,CAAC;AACpD,OAAO,EAAE,IAAI,EAAE,MAAM,WAAW,CAAC;AACjC,OAAO,EAAE,aAAa,EAAE,gBAAgB,EAAE,MAAM,YAAY,CAAC;AAE7D;;;;;;;GAOG;AACH,MAAM,CAAC,KAAK,UAAU,UAAU,CAC9B,MAAc,EACd,YAAoB,EACpB,SAAkB,EAClB,YAAoB,MAAM;IAE1B,MAAM,GAAG,GAAG,aAAa,CAAC,SAAS,CAAC,CAAC;IACrC,MAAM,KAAK,CAAC,GAAG,EAAE,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC;IAEtC,MAAM,SAAS,GAAG,IAAI,IAAI,EAAE;SACzB,WAAW,EAAE;SACb,OAAO,CAAC,OAAO,EAAE,GAAG,CAAC;SACrB,OAAO,CAAC,GAAG,EAAE,GAAG,CAAC;SACjB,KAAK,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;IAEhB,MAAM,QAAQ,GAAG,gBAAgB,CAAC,YAAY,CAAC,CAAC;IAChD,MAAM,QAAQ,GAAG,GAAG,QAAQ,IAAI,SAAS,IAAI,SAAS,EAAE,CAAC;IACzD,MAAM,QAAQ,GAAG,IAAI,CAAC,GAAG,EAAE,QAAQ,CAAC,CAAC;IAErC,MAAM,MAAM,GAAG,MAAM,CAAC,IAAI,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAC;IAC7C,MAAM,SAAS,CAAC,QAAQ,EAAE,MAAM,CAAC,CAAC;IAElC,OAAO,QAAQ,CAAC;AAClB,CAAC"}

package/dist/providers/direct/index.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/providers/direct/index.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EACV,SAAS,EACT,sBAAsB,EACtB,aAAa,EACb,aAAa,EACb,UAAU,EAGX,MAAM,aAAa,CAAC;AA6GrB,qBAAa,cAAe,YAAW,SAAS;IACxC,gBAAgB,CAAC,MAAM,EAAE,sBAAsB,GAAG,OAAO,CAAC,UAAU,CAAC;IAuGrE,YAAY,CAAC,OAAO,EAAE,aAAa,GAAG,OAAO,CAAC,UAAU,CAAC;IAMzD,WAAW,CAAC,OAAO,EAAE,aAAa,GAAG,OAAO,CAAC,UAAU,CAAC;CAK/D"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/providers/direct/index.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EACV,SAAS,EACT,sBAAsB,EACtB,aAAa,EACb,aAAa,EACb,UAAU,EAGX,MAAM,aAAa,CAAC;AAgHrB,qBAAa,cAAe,YAAW,SAAS;IACxC,gBAAgB,CAAC,MAAM,EAAE,sBAAsB,GAAG,OAAO,CAAC,UAAU,CAAC;IA8GrE,YAAY,CAAC,OAAO,EAAE,aAAa,GAAG,OAAO,CAAC,UAAU,CAAC;IAMzD,WAAW,CAAC,OAAO,EAAE,aAAa,GAAG,OAAO,CAAC,UAAU,CAAC;CAK/D"}