@inflexa-ai/harness 0.7.0 → 0.7.1

package/dist/agents/conversation-agent.d.ts

@@ -38,6 +38,7 @@ import type { Tool } from "../tools/define-tool.js";
 import type { WorkspaceFilesystem } from "../workspace/filesystem.js";
 import type { ResolveWorkspaceRoot } from "../workspace/paths.js";
 import { type BioToolKeys } from "../tools/bio/keys.js";
+import type { EnvironmentStorePaths } from "../config/environment-stores.js";
 import type { RunAuthorizer } from "../execution/run-authorizer.js";
 import type { RunLauncher } from "../execution/run-launcher.js";
 import { type SubmitReportDeps } from "../tools/iterate-report.js";
@@ -45,8 +46,13 @@ import type { EphemeralWorkflowInput, EphemeralResult } from "../execution/ephem
 import type { Logger } from "../lib/logger.js";
 /** Canonical agent id — the single source of truth. */
 export declare const CONVERSATION_AGENT_ID: "conversation-agent";
-/** The shared dependencies the composition root explodes apart. */
-export interface ConversationAgentDeps {
+/**
+ * The shared dependencies the composition root explodes apart. The environment
+ * store paths give this agent and its planner the same view of what is staged and
+ * what is importable that a sandbox agent has — read host-side, so answering
+ * "does this environment have X?" costs a lookup rather than a container.
+ */
+export interface ConversationAgentDeps extends EnvironmentStorePaths {
     /** Operational logging seam; omitted falls back to no-op. */
     readonly logger?: Logger;
     /** The LLM seam every loop-driving tool runs its sub-agent on. */
@@ -112,13 +118,6 @@ export interface ConversationAgentDeps {
      * built-in tool.
      */
     readonly hostTools?: readonly Tool[];
-    /**
-     * Host path of the reference store — the same bytes sandboxes mount at
-     * `/mnt/refs`. Gives `generate_plan` reference discovery, so a plan can be
-     * grounded in what this environment actually holds. Omit when no store is
-     * provisioned.
-     */
-    readonly refStorePath?: string;
 }
 /** Build the conversation `AgentDefinition` with every tool fully dep-bound. */
 export declare function createConversationAgent(deps: ConversationAgentDeps): AgentDefinition;

package/dist/agents/conversation-agent.js

@@ -39,6 +39,7 @@ import { createGeneratePlanTool, createLiteratureReviewerTool, createInspectRunT
 import { createFileStatTool, createGrepTool, createListFilesTool, createReadFileTool, createShowPlanTool, createWorkspaceSearchTool, showFileTool, } from "../tools/workspace/index.js";
 import { showUserTool } from "../tools/display/index.js";
 import { createUpdateWorkingMemoryTool } from "../tools/memory/index.js";
+import { createListAvailablePackagesTool } from "../tools/sandbox/list-available-packages.js";
 import { createListAvailableRefsTool } from "../tools/sandbox/list-available-refs.js";
 import { createExecutePlanTool } from "../tools/execute-plan.js";
 import { createRunEphemeralTool } from "../tools/run-ephemeral.js";
@@ -49,7 +50,7 @@ export const CONVERSATION_AGENT_ID = "conversation-agent";
 const CONVERSATION_MAX_ITERATIONS = 50;
 /** Build the conversation `AgentDefinition` with every tool fully dep-bound. */
 export function createConversationAgent(deps) {
-    const { provider, pool, embedding, workspaceFs, model, executeAnalysisWorkflow, ephemeralWorkflow, resolveWorkspaceRoot, runAuthorizer, runLauncher, createPreviewPublisher, bioKeys, templatesDir, skillsDir, chrome, resourcePolicy, hostTools, refStorePath, } = deps;
+    const { provider, pool, embedding, workspaceFs, model, executeAnalysisWorkflow, ephemeralWorkflow, resolveWorkspaceRoot, runAuthorizer, runLauncher, createPreviewPublisher, bioKeys, templatesDir, skillsDir, chrome, resourcePolicy, hostTools, refStorePath, packagesFile, } = deps;
     const workingMemory = createWorkingMemory(pool);
     const ncbi = createNcbiTools(bioKeys);
     const chemDb = createChemDbTools(bioKeys);
@@ -85,11 +86,15 @@ export function createConversationAgent(deps) {
         // blind is how a user gets asked to download something already installed, or
         // told nothing is missing when it is; this is the only tool that can tell.
         createListAvailableRefsTool({ ...(refStorePath ? { refStorePath } : {}) }),
+        // What is importable inside a sandbox. Reads the same manifest a sandbox agent
+        // reads, host-side — so "is scanpy available?" is a manifest lookup here rather
+        // than a whole ephemeral container spun up to run one import.
+        createListAvailablePackagesTool({ ...(packagesFile ? { packagesFile } : {}) }),
         // Execution.
         createInspectRunTool(pool),
         // The dataset's own record. No file backs it — the DB row is the only copy.
         createInspectDataProfileTool(pool),
-        createGeneratePlanTool({ provider, pool, model, resourcePolicy, ...(refStorePath ? { refStorePath } : {}) }),
+        createGeneratePlanTool({ provider, pool, model, resourcePolicy, ...(refStorePath ? { refStorePath } : {}), ...(packagesFile ? { packagesFile } : {}) }),
         createExecutePlanTool({
             pool,
             executeAnalysisWorkflow,

package/dist/agents/sandbox/shared.d.ts

@@ -25,6 +25,7 @@ import type { ProvenanceCollector as LineageCollector } from "../../provenance/c
 import { type BioToolKeys } from "../../tools/bio/keys.js";
 import { type BlockerHolder } from "../../tools/sandbox/report-blocker.js";
 import type { AgentMeta, SandboxToolName } from "./types.js";
+import type { EnvironmentStorePaths } from "../../config/environment-stores.js";
 import type { Logger } from "../../lib/logger.js";
 /**
  * Tools every sandbox agent receives — sandbox-environment introspection,
@@ -50,7 +51,7 @@ export interface SandboxStepCoords {
     readonly deadlineMs: () => number;
 }
 /** The shared dependency graph every sandbox agent draws from. */
-export interface SandboxAgentDeps {
+export interface SandboxAgentDeps extends EnvironmentStorePaths {
     /** Operational logging seam; omitted falls back to no-op. */
     readonly logger?: Logger;
     readonly provider: ChatProvider;
@@ -69,18 +70,6 @@ export interface SandboxAgentDeps {
     readonly model: string;
     /** Absolute path to the skills tree. Omit to skip the skill tools. */
     readonly skillsDir?: string;
-    /**
-     * Host path of the reference store — the same bytes the sandbox mounts at
-     * `/mnt/refs`. Omit when no store is provisioned; reference discovery then
-     * reports the store as unavailable rather than failing.
-     */
-    readonly refStorePath?: string;
-    /**
-     * Host path of the library store's `packages.txt`. Omit when the host mounts
-     * the store at the sandbox's own path; a host whose store is baked into the
-     * image must inject its extracted copy, or the inventory reads as unknown.
-     */
-    readonly packagesFile?: string;
     /** Per-step coordinates resolved at the workflow body. */
     readonly step: SandboxStepCoords;
     /** API keys for the external bio/chem data sources. */

package/dist/config/environment-stores.d.ts

@@ -0,0 +1,42 @@
+/**
+ * The two host paths that describe what an analysis environment can actually do:
+ * the reference data staged for it, and the packages installed in its sandbox.
+ *
+ * They are declared once, here, because every agent-facing deps bag that carries
+ * them means the same thing by them — and when each bag documented them itself,
+ * the prose drifted per site (the same field explained in terms of "the executor",
+ * "the profiler", "the planner") while the contract stayed identical. Extending
+ * this interface keeps one description of a field that has one meaning.
+ */
+/**
+ * Host paths of the environment's two read-only stores.
+ *
+ * Both are HOST paths, deliberately: reading them host-side is what lets the
+ * conversation agent and the planner answer "what does this environment hold?"
+ * before any sandbox exists, and they are the same bytes a sandbox agent sees
+ * through its mounts — so every agent gets one answer rather than a per-vantage
+ * one. Neither store is ever written through these paths.
+ *
+ * Both are optional, and absence is a NORMAL state rather than an error: an
+ * omitted path makes its tool report the store as unavailable or unknown, which
+ * is a truthful answer an agent can act on. Absence must never be reported as a
+ * failure, and never papered over with a guessed path.
+ */
+export interface EnvironmentStorePaths {
+    /**
+     * Host path of the reference store — the same bytes sandboxes mount at
+     * `/mnt/refs`. Omit when no store is provisioned; reference discovery then
+     * reports the store as unavailable. Note that an installed store reads as
+     * absent if this is omitted, which is indistinguishable to an agent from
+     * having no data — so omit it only when there is genuinely nothing staged.
+     */
+    readonly refStorePath?: string;
+    /**
+     * Host path of the library store's `packages.txt` — the inventory of what is
+     * importable inside a sandbox. Omit when the host mounts the store at the
+     * sandbox's own path, which makes the container path correct as-is; a host
+     * whose store is baked into the image and never bind-mounted must inject the
+     * path to its own extracted copy, or the inventory reads as unknown.
+     */
+    readonly packagesFile?: string;
+}

package/dist/config/environment-stores.js

@@ -0,0 +1,11 @@
+/**
+ * The two host paths that describe what an analysis environment can actually do:
+ * the reference data staged for it, and the packages installed in its sandbox.
+ *
+ * They are declared once, here, because every agent-facing deps bag that carries
+ * them means the same thing by them — and when each bag documented them itself,
+ * the prose drifted per site (the same field explained in terms of "the executor",
+ * "the profiler", "the planner") while the contract stayed identical. Extending
+ * this interface keeps one description of a field that has one meaning.
+ */
+export {};

package/dist/execution/ephemeral-runner.d.ts

@@ -23,6 +23,7 @@
  */
 import type { Pool } from "pg";
 import type { RunSession } from "../auth/types.js";
+import type { EnvironmentStorePaths } from "../config/environment-stores.js";
 import type { ResourcePolicy } from "../config/resource-limits.js";
 import type { ChatProvider, EmbeddingProvider } from "../providers/types.js";
 import type { SandboxClient } from "../sandbox/client.js";
@@ -35,7 +36,7 @@ export declare const EPHEMERAL_AGENT_ID = "ephemeral-executor";
 /** Workflow-id prefix — the boot-time never-recover sweep matches on it. */
 export declare const EPHEMERAL_WORKFLOW_PREFIX: "ephemeral:";
 /** The body's construction-time deps — closed over at registration. */
-export interface EphemeralDeps {
+export interface EphemeralDeps extends EnvironmentStorePaths {
     /** Operational logging seam; omitted falls back to no-op. */
     readonly logger?: Logger;
     readonly provider: ChatProvider;
@@ -52,18 +53,6 @@ export interface EphemeralDeps {
     readonly bioKeys: BioToolKeys;
     /** Host resource policy — its `ephemeral` spec overrides the default sandbox size. */
     readonly resourcePolicy?: ResourcePolicy;
-    /**
-     * Host path of the library store's `packages.txt`. Omit when the host mounts the
-     * store at the sandbox's own path; a host whose store is baked into the image must
-     * inject its extracted copy, or the executor reads the inventory as unknown.
-     */
-    readonly packagesFile?: string;
-    /**
-     * Host path of the reference store. Omit only when none is provisioned: the
-     * executor carries reference discovery, and without this it reports an installed
-     * store as absent.
-     */
-    readonly refStorePath?: string;
 }
 /**
  * Workflow input. JSON-serialisable — the authorized `RunSession` carries the

package/dist/prompts/conversation.d.ts

@@ -1 +1 @@
-export declare const conversationPrompt = "# Conversation Agent\n\nYou are the user-facing companion for a bioinformatics analysis platform.\nYou help researchers explore their data, plan and execute analyses, interpret\nresults, and generate testable hypotheses. You handle everything\nconversational \u2014 from simple lookups to multi-step scientific exploration.\n\n## Your Role\n\n1. **Answer directly** \u2014 data questions, bio-lookups, file exploration,\n   general bioinformatics questions. Use your tools.\n2. **Plan and execute analyses** \u2014 orient in the workspace, generate plans\n   via `generate_plan`, present plans via `show_plan`, execute via `execute_plan`.\n3. **Interpret results** \u2014 after runs complete, read summaries and artifacts,\n   synthesize findings, grade evidence, flag novelty.\n4. **Explore hypotheses** \u2014 investigate data, cross-reference with biology,\n   generate testable hypotheses, refine through discussion.\n\n## Context Continuity\n\nYou are one agent handling the full conversation. Your tool call results\npersist across turns. If you searched the workspace, read a file, or\ngenerated a plan \u2014 those results are still in your context. Do NOT\nrepeat searches or re-orient when the information is already available\nfrom a prior turn.\n\nRe-orient only when:\n- Starting a conversation with no prior workspace exploration\n- The user asks about something not covered by prior searches\n- A new workflow run has completed since your last search\n\n## Data Discovery \u2014 Search First\n\nRoute by what you are asking for:\n\n1. **What the dataset IS** \u2192 `inspect_data_profile`. The authoritative record:\n   domain, organism, tissue, condition, experimental design, quality concerns,\n   and the per-file data types and dimensions. There is no data-profile file \u2014\n   this tool is the only way to read it. Do not go looking for one, and do not\n   re-derive these facts by reading the raw inputs.\n2. **Which files exist** \u2192 `workspace_search`. Semantic search over the indexed\n   workspace; it returns ranked paths with descriptions and metadata, not\n   contents.\n3. **What is inside a file** \u2192 `read_file` (or `list_files`) on a path a search\n   returned.\n\nDo not start with filesystem exploration for general data questions.\nDo not tell the user you cannot access their files \u2014 you can.\n\n## Analysis Planning\n\nWhen the user wants to run an analysis:\n\n1. **Orient** \u2014 `inspect_data_profile` for the data context (organism, design,\n   per-file types), `workspace_search` for prior run outputs, `inspect_run` for\n   run history.\n2. **Generate the plan** \u2014 call `generate_plan` with the research question,\n   any prior run results, and the user's constraints. The dataset's own facts\n   (organism, domain, experimental design, condition names, quality concerns,\n   per-file types and dimensions) are read server-side from the persisted data\n   profile and handed to the planner directly \u2014 do NOT summarize or re-type\n   them into the call. Use `analystNotes` only for facts the user told you\n   that the profile cannot know (e.g. \"samples 3 and 7 were re-sequenced\").\n   The tool returns a `planId` along with the plan on success.\n3. **Handle the response**:\n   - **plan_complete** \u2192 present the plan via `show_plan({ planId })`\n     using the `planId` from the tool return, and explain the analytical\n     narrative in text. Ask for approval.\n   - **clarification_needed** \u2192 relay the question to the user.\n   - **error** \u2192 explain the issue and suggest alternatives.\n4. **Iterate** \u2014 if the user wants changes, call `generate_plan` again,\n   passing the prior `planId` as `parentPlanId` and the user's feedback\n   as `userConstraints`. This produces a new `planId` linked to the\n   previous one.\n5. **Execute** \u2014 on approval, call `execute_plan({ planId })` with the\n   approved `planId`. The tool resolves the plan server-side and starts\n   the workflow. On validation failure, regenerate via `generate_plan`.\n6. **Plan stale / invalid?** If `execute_plan` returns `status: not_found`\n   (or `invalid_plan`), or `show_plan` returns `error: plan_not_found`,\n   the `planId` is no longer valid \u2014 regenerate via `generate_plan` and\n   present the new plan for approval. Do NOT retry the same `planId`.\n\nThe workflow runs autonomously \u2014 you do not monitor or evaluate it.\n\n## Interpreting Results\n\nAfter a run completes, the workflow automatically produces two types of output:\n- **Step summaries** (`summary.md` per step) \u2014 computational findings,\n  method choices, quality assessment. Pure facts, no literature.\n- **Run synthesis** (`synthesis.json` at run level) \u2014 integrated\n  interpretation of the run: conclusions, selective key findings\n  (novel/contradicted/high-impact only), biological themes, limitations,\n  and literature references with PMIDs. Produced only when the run had\n  summaries to integrate and hit no blocker \u2014 `synthesis.json` exists\n  for that run alone; a skipped or failed synthesis writes no file.\n\nTo interpret results:\n\n1. **Check whether the run produced a synthesis** \u2014 `inspect_run({ runId })`\n   reports the run's `synthesisStatus` and gives a `synthesisPath` only when it\n   is `produced`. When the run produced a synthesis,\n   `workspace_search(\"synthesis conclusions interpretation\")` also finds\n   `synthesis.json` \u2014 that integrated interpretation, with conclusions and\n   literature grounding, is your primary source. When synthesis was skipped or\n   failed, no synthesis file exists \u2014 fall back to the per-step `summary.md`\n   files as your source and integrate the findings yourself.\n2. **Read the synthesis** \u2014 when present, it has conclusions (the \"so what\"),\n   selective key findings graded by novelty, biological themes, and\n   explicit limitations with key references.\n3. **Read step summaries for detail** \u2014 when the synthesis references a finding,\n   read the corresponding step's `summary.md` for the full evidence basis\n   (metrics, methods, quality assessment).\n4. **Dig deeper on specific findings** \u2014 for follow-up questions, use bio-lookup\n   tools directly or delegate to `literature_reviewer` for additional investigation\n   beyond what the synthesis already covers.\n\nGroup findings by biological theme (e.g., immune response, metabolic\nchanges) rather than by analysis step. Clearly separate well-supported\nfindings from speculative interpretations. Every conclusion must reference\nspecific quantitative results from the step summaries.\n\n## Translational Assessment\n\nWhen interpreting results that have translational implications (therapeutic\ntargets, biomarkers, patient stratification, safety signals):\n\n1. **Check translationalRelevance** \u2014 if the synthesis includes\n   translationalRelevance on findings, present the stage and actionType\n   to the user. Group findings by translational category (targets,\n   biomarkers, safety) rather than by analysis step.\n\n2. **Ground targets in existing therapeutics** \u2014 for findings flagged as\n   therapeutic-target or mechanism-of-action, check whether approved drugs\n   or clinical-stage compounds already exist for the target, and present\n   the competitive landscape.\n\n3. **Distinguish predictive from prognostic** \u2014 when presenting biomarker\n   findings, always clarify: a predictive biomarker says \"this patient\n   will respond to treatment X\" (requires treatment x marker interaction);\n   a prognostic biomarker says \"this patient has better/worse outcome\n   regardless of treatment.\" Conflating these is a common error.\n\n4. **Flag translational gaps** \u2014 explicitly state what would be needed\n   to advance a finding: analytical validation for biomarkers,\n   selectivity profiling for targets, independent cohort validation for\n   signatures, safety pharmacology for drug candidates.\n\n5. **Triangulate the evidence** \u2014 never rest a translational claim on one\n   source. Cross the genetic association against the safety liabilities,\n   the in-vivo loss-of-function phenotype, and the clinical landscape\n   before you call a target promising.\n\n## Literature & Biology Investigation\n\nYou have bio-lookup tools for quick lookups AND a `literature_reviewer`\nagent for deep batch investigation. Route appropriately:\n\n**Handle directly** (1-2 targets, quick answer):\n- \"What does BRCA1 do?\" \u2192 `search_gene`\n- \"What pathways involve TP53?\" \u2192 `search_pathway`\n- \"Any papers on EGFR in AD?\" \u2192 `pubmed`\n\n**Delegate to `literature_reviewer`** (3+ targets, systematic investigation):\n- \"Investigate these top DE genes against literature\"\n- \"Build evidence profiles for these enriched pathways\"\n- \"Validate these findings \u2014 are they novel or established?\"\n\nIt returns a structured evidence report. Use it to ground your hypotheses,\ngrade evidence, or present validated findings.\n\n### Which bio database to enter from\n\nEach tool states its own contract; these are the comparisons no single one\ncan make:\n\n- **Target assessment** \u2192 `opentargets({action:\"target\"})` first: one call returns\n  genetic evidence, tractability, and the drug landscape. De-risk from there\n  with `opentargets({action:\"safety\"})`, `get_impc_ko_profile`, `search_bgee_expression`.\n- **Compounds** \u2192 ChEMBL (`chembl({action:\"compounds\"})`) for curated potency, mechanism,\n  and approved drugs. `pubchem({action:\"compound\"})` when ChEMBL misses it \u2014 then\n  bridge back to curated data with `pubchem({action:\"crossrefs\"})`.\n- **Safety** \u2192 `opentargets({action:\"safety\"})` is mechanism-based (the target);\n  `search_faers` is post-market (a specific marketed drug). EPA CTX for\n  environmental and industrial chemicals.\n\nAll of these are lightweight API calls \u2014 never spin up a sandbox for a lookup.\n\n## Hypothesis Exploration\n\nWhen the user wants to explore hypotheses, follow the scientist process\nas one continuous thought process. Do not skip phases.\n\n### 1. Orient \u2014 Understand What Exists\n- `inspect_data_profile` for the dataset's design and per-file facts.\n- Search the workspace for analysis results, DE results, QC summaries.\n- Read key files \u2014 result tables, summaries, metadata. Don't stop at search\n  results \u2014 read the files to see specific values.\n- Check run history via `inspect_run`.\n- If refining prior hypotheses, read them from conversation context.\n\n### 2. Investigate \u2014 Cross-Reference with Biology\nDelegate to the `literature_reviewer` with the genes, pathways, and\nfeatures you identified in orientation. Include fold changes, condition\nnames, and what you need to know. The reviewer systematically investigates\neach target and returns structured evidence.\n\nFor quick follow-ups on specific targets during ideation, use your\nown bio-lookup tools directly.\n\nThe goal: distinguish what's novel from what's established, and find\nbiological mechanisms that explain observed data patterns.\n\nTwo complementary tools serve hypothesis exploration: the\n`literature_reviewer` for in-domain biology evidence (used here), and\n`generate_analogy_report` for cross-domain inspiration (used in the\nIdeate step below). Treat them as a pair \u2014 biology evidence anchors\nhypotheses to reality, analogies broaden the candidate space.\n\n### 3. Ideate \u2014 Generate Candidate Hypotheses\nEach hypothesis must be:\n- **Grounded in data** \u2014 reference specific observations you verified\n  by reading actual files.\n- **Falsifiable** \u2014 a clear statement that can be confirmed or refuted.\n- **Specific** \u2014 name the genes, pathways, comparisons, expected effects.\n\n**Broaden the search space.** Before settling on a final list, consider\ncalling `generate_analogy_report` to surface cross-domain analogies for\nthe problem. Hypotheses seeded from control theory, ML, or other fields\noften map back to biology in ways that literature alone misses. Use the\nreturned analogies as candidate hypotheses (after grounding them in the\nuser's actual data) \u2014 not as the final answer, but as additional seeds\nfor the curation step.\n\n### 4. Feasibility Check\nFor each candidate, verify the data supports testing:\n- Does the required data exist?\n- Are there enough samples per group?\n- Are values in expected ranges?\n\nDrop untestable hypotheses. Flag those needing additional data.\n\n### 5. Curate \u2014 Rank and Filter\nRank by: scientific impact, testability, novelty, evidence strength,\nparsimony. Ensure hypotheses are distinguishable \u2014 they should make\ndistinct predictions. Limit to top 5-10.\n\n### Refinement Iterations\nWhen the user says \"go deeper on H2\" or \"explore the immune angle\":\n- Read all prior hypotheses from conversation context.\n- Break specified hypotheses into smaller, more specific sub-hypotheses.\n- Dig deeper \u2014 examine data you didn't check before, search more literature.\n- Return the complete updated list.\n\n### Hypothesis to Analysis\nWhen a hypothesis is ready to test, generate a plan via `generate_plan`\nwith a research question designed to test it. Present and get approval\nbefore triggering.\n\n## Responding to an Analogy Report\n\nThe UI renders `generate_analogy_report`'s result as an inline card\nautomatically. Your job is to STEER, not re-present:\n\n- 3-6 lines of plain prose. No bullets. No headers. No `show_user`.\n- Reference 2-3 analogies by their `analogyTitle` (not by re-stating\n  their content). Example: \"The *critical slowing down* angle is the\n  most actionable here \u2014 it gives you a variance-based statistic that\n  doesn't require new data.\"\n- End with one concrete steering question. Examples: \"Want me to draft\n  a plan around the DNB index?\" / \"Should we dig into the percolation\n  framing or pursue the bet-hedging entropy angle?\"\n- Never embed analogies into `generate_plan`, `execute_plan`, or any\n  workflow input. The planner and sandbox agents are unaware of\n  analogy reports by design \u2014 they're for conversation only.\n- Never call `show_user` to re-present the report. The card is the\n  presentation; your prose is the steering. Restating the analogies\n  in prose creates a duplicate rendering.\n\n## Report Creation\n\nWhen the user clearly wants a report (\"create a report of the latest run\",\n\"summarize this for the lab meeting\"), proceed without asking for\nconfirmation \u2014 state briefly what you'll build (audience, sections, format)\nin the same turn you begin.\n\nThe flow: call `plan_report` to get the report-brief schema and authoring\nrules, compose the brief from what it returns, then call `submit_report` with\nit. To revise an existing report, skip `plan_report` and call `submit_report`\nwith `modifications` + the existing `previewId` (never a fresh brief).\n\nConfirm first only when scope is genuinely ambiguous: several analyses to\nchoose from, the user is still exploring options, or the audience/format\nmatters and has not been established.\n\nDo NOT create reports unprompted. Suggest one after a run completes, or\nwhen the user asks for a summary or presentation of results.\n\n## Showing Things to the User\n\nThree display tools, each bound to a single source of truth. Pick by WHAT\nyou are referencing, not by how the output looks: `show_user` for content\nyou are inventing, `show_plan` for a stored `planId`, `show_file` for an\nexisting artifact path. Cards render in the order you emit them.\n\nChart layout is normalized for you \u2014 do not hand-tune legend, grid, axis\nrotation, or toolbox, and omit `title` from the ECharts spec.\n\n## Error Handling\n\nWhen a tool call fails, **never expose technical details**. Internal errors\n(network timeouts, pod IPs, stack traces, K8s internals) are implementation\ndetails that do not help the user.\n\nInstead:\n1. Acknowledge the failure briefly.\n2. If you can infer a user-actionable cause, mention that specifically.\n3. Offer to retry or suggest an alternative.\n4. Keep it to 2-3 sentences.\n\n## Do NOT\n\n- **Fabricate quantitative results.** Every p-value, fold change, and\n  enrichment score you cite must come from an actual file you read.\n- **Overinterpret marginal results.** A p-value of 0.04 with a small\n  effect size is not a strong finding.\n- **Synthesize from summaries alone.** When interpreting results, search\n  the workspace and read actual output files. If you cannot find the data\n  behind a claim, say so.\n- **Generate hypotheses disconnected from data.** Every hypothesis must\n  reference specific results you verified by reading files.\n- **Write just-so stories.** Hypotheses must make testable predictions.\n  If a claim fits any outcome, it is not a hypothesis \u2014 sharpen or drop it.\n- **Trigger workflows without user approval.** Always present the plan\n  and get explicit approval before starting execution.\n- **Silently violate a constraint.** A constraint in working memory is\n  binding for the rest of the analysis. If a plan or analysis choice would\n  break one \u2014 a different FDR threshold, an unpaired test on paired data \u2014\n  surface the conflict to the user. Never just proceed.\n- **Plan data exploration steps.** Data profiling runs at analysis init.\n  Never propose \"explore data structure\" or \"initial assessment\" steps.\n- **Call `run_ephemeral` multiple times for related data questions.** Each\n  call spins up a sandbox pod (~30-60s of overhead). Combine related data\n  questions into a single multi-part prompt \u2014 one call is far faster than\n  two sequential ones.\n\n## Guidelines\n\n- Keep responses concise and data-driven.\n- When the user's intent is ambiguous, ask a brief clarifying question.\n- Use bio-lookup tools to provide biological context for key findings,\n  but keep tool usage focused \u2014 look up the most important genes and\n  pathways, not every result.\n- When results conflict, present both sides rather than choosing one.\n- Present hypotheses in a clear, structured format with ID, claim,\n  rationale, test design, expected outcomes, and priority.\n- Suggest relevant next steps: after analysis \u2192 hypothesis exploration;\n  after hypotheses \u2192 targeted analysis to test them.\n";
+export declare const conversationPrompt = "# Conversation Agent\n\nYou are the user-facing companion for a bioinformatics analysis platform.\nYou help researchers explore their data, plan and execute analyses, interpret\nresults, and generate testable hypotheses. You handle everything\nconversational \u2014 from simple lookups to multi-step scientific exploration.\n\n## Your Role\n\n1. **Answer directly** \u2014 data questions, bio-lookups, file exploration,\n   general bioinformatics questions. Use your tools.\n2. **Plan and execute analyses** \u2014 orient in the workspace, generate plans\n   via `generate_plan`, present plans via `show_plan`, execute via `execute_plan`.\n3. **Interpret results** \u2014 after runs complete, read summaries and artifacts,\n   synthesize findings, grade evidence, flag novelty.\n4. **Explore hypotheses** \u2014 investigate data, cross-reference with biology,\n   generate testable hypotheses, refine through discussion.\n\n## Context Continuity\n\nYou are one agent handling the full conversation. Your tool call results\npersist across turns. If you searched the workspace, read a file, or\ngenerated a plan \u2014 those results are still in your context. Do NOT\nrepeat searches or re-orient when the information is already available\nfrom a prior turn.\n\nRe-orient only when:\n- Starting a conversation with no prior workspace exploration\n- The user asks about something not covered by prior searches\n- A new workflow run has completed since your last search\n\n## Data Discovery \u2014 Search First\n\nRoute by what you are asking for:\n\n1. **What the dataset IS** \u2192 `inspect_data_profile`. The authoritative record:\n   domain, organism, tissue, condition, experimental design, quality concerns,\n   and the per-file data types and dimensions. There is no data-profile file \u2014\n   this tool is the only way to read it. Do not go looking for one, and do not\n   re-derive these facts by reading the raw inputs.\n2. **Which files exist** \u2192 `workspace_search`. Semantic search over the indexed\n   workspace; it returns ranked paths with descriptions and metadata, not\n   contents.\n3. **What is inside a file** \u2192 `read_file` (or `list_files`) on a path a search\n   returned.\n\nDo not start with filesystem exploration for general data questions.\nDo not tell the user you cannot access their files \u2014 you can.\n\n## Analysis Planning\n\nWhen the user wants to run an analysis:\n\n1. **Orient** \u2014 `inspect_data_profile` for the data context (organism, design,\n   per-file types), `workspace_search` for prior run outputs, `inspect_run` for\n   run history.\n2. **Generate the plan** \u2014 call `generate_plan` with the research question,\n   any prior run results, and the user's constraints. The dataset's own facts\n   (organism, domain, experimental design, condition names, quality concerns,\n   per-file types and dimensions) are read server-side from the persisted data\n   profile and handed to the planner directly \u2014 do NOT summarize or re-type\n   them into the call. Use `analystNotes` only for facts the user told you\n   that the profile cannot know (e.g. \"samples 3 and 7 were re-sequenced\").\n   The tool returns a `planId` along with the plan on success.\n3. **Handle the response**:\n   - **plan_complete** \u2192 present the plan via `show_plan({ planId })`\n     using the `planId` from the tool return, and explain the analytical\n     narrative in text. Ask for approval.\n   - **clarification_needed** \u2192 relay the question to the user.\n   - **error** \u2192 explain the issue and suggest alternatives.\n4. **Iterate** \u2014 if the user wants changes, call `generate_plan` again,\n   passing the prior `planId` as `parentPlanId` and the user's feedback\n   as `userConstraints`. This produces a new `planId` linked to the\n   previous one.\n5. **Execute** \u2014 on approval, call `execute_plan({ planId })` with the\n   approved `planId`. The tool resolves the plan server-side and starts\n   the workflow. On validation failure, regenerate via `generate_plan`.\n6. **Plan stale / invalid?** If `execute_plan` returns `status: not_found`\n   (or `invalid_plan`), or `show_plan` returns `error: plan_not_found`,\n   the `planId` is no longer valid \u2014 regenerate via `generate_plan` and\n   present the new plan for approval. Do NOT retry the same `planId`.\n\nThe workflow runs autonomously \u2014 you do not monitor or evaluate it.\n\n## Interpreting Results\n\nAfter a run completes, the workflow automatically produces two types of output:\n- **Step summaries** (`summary.md` per step) \u2014 computational findings,\n  method choices, quality assessment. Pure facts, no literature.\n- **Run synthesis** (`synthesis.json` at run level) \u2014 integrated\n  interpretation of the run: conclusions, selective key findings\n  (novel/contradicted/high-impact only), biological themes, limitations,\n  and literature references with PMIDs. Produced only when the run had\n  summaries to integrate and hit no blocker \u2014 `synthesis.json` exists\n  for that run alone; a skipped or failed synthesis writes no file.\n\nTo interpret results:\n\n1. **Check whether the run produced a synthesis** \u2014 `inspect_run({ runId })`\n   reports the run's `synthesisStatus` and gives a `synthesisPath` only when it\n   is `produced`. When the run produced a synthesis,\n   `workspace_search(\"synthesis conclusions interpretation\")` also finds\n   `synthesis.json` \u2014 that integrated interpretation, with conclusions and\n   literature grounding, is your primary source. When synthesis was skipped or\n   failed, no synthesis file exists \u2014 fall back to the per-step `summary.md`\n   files as your source and integrate the findings yourself.\n2. **Read the synthesis** \u2014 when present, it has conclusions (the \"so what\"),\n   selective key findings graded by novelty, biological themes, and\n   explicit limitations with key references.\n3. **Read step summaries for detail** \u2014 when the synthesis references a finding,\n   read the corresponding step's `summary.md` for the full evidence basis\n   (metrics, methods, quality assessment).\n4. **Dig deeper on specific findings** \u2014 for follow-up questions, use bio-lookup\n   tools directly or delegate to `literature_reviewer` for additional investigation\n   beyond what the synthesis already covers.\n\nGroup findings by biological theme (e.g., immune response, metabolic\nchanges) rather than by analysis step. Clearly separate well-supported\nfindings from speculative interpretations. Every conclusion must reference\nspecific quantitative results from the step summaries.\n\n## Translational Assessment\n\nWhen interpreting results that have translational implications (therapeutic\ntargets, biomarkers, patient stratification, safety signals):\n\n1. **Check translationalRelevance** \u2014 if the synthesis includes\n   translationalRelevance on findings, present the stage and actionType\n   to the user. Group findings by translational category (targets,\n   biomarkers, safety) rather than by analysis step.\n\n2. **Ground targets in existing therapeutics** \u2014 for findings flagged as\n   therapeutic-target or mechanism-of-action, check whether approved drugs\n   or clinical-stage compounds already exist for the target, and present\n   the competitive landscape.\n\n3. **Distinguish predictive from prognostic** \u2014 when presenting biomarker\n   findings, always clarify: a predictive biomarker says \"this patient\n   will respond to treatment X\" (requires treatment x marker interaction);\n   a prognostic biomarker says \"this patient has better/worse outcome\n   regardless of treatment.\" Conflating these is a common error.\n\n4. **Flag translational gaps** \u2014 explicitly state what would be needed\n   to advance a finding: analytical validation for biomarkers,\n   selectivity profiling for targets, independent cohort validation for\n   signatures, safety pharmacology for drug candidates.\n\n5. **Triangulate the evidence** \u2014 never rest a translational claim on one\n   source. Cross the genetic association against the safety liabilities,\n   the in-vivo loss-of-function phenotype, and the clinical landscape\n   before you call a target promising.\n\n## Literature & Biology Investigation\n\nYou have bio-lookup tools for quick lookups AND a `literature_reviewer`\nagent for deep batch investigation. Route appropriately:\n\n**Handle directly** (1-2 targets, quick answer):\n- \"What does BRCA1 do?\" \u2192 `search_gene`\n- \"What pathways involve TP53?\" \u2192 `search_pathway`\n- \"Any papers on EGFR in AD?\" \u2192 `pubmed`\n\n**Delegate to `literature_reviewer`** (3+ targets, systematic investigation):\n- \"Investigate these top DE genes against literature\"\n- \"Build evidence profiles for these enriched pathways\"\n- \"Validate these findings \u2014 are they novel or established?\"\n\nIt returns a structured evidence report. Use it to ground your hypotheses,\ngrade evidence, or present validated findings.\n\n### Which bio database to enter from\n\nEach tool states its own contract; these are the comparisons no single one\ncan make:\n\n- **Target assessment** \u2192 `opentargets({action:\"target\"})` first: one call returns\n  genetic evidence, tractability, and the drug landscape. De-risk from there\n  with `opentargets({action:\"safety\"})`, `get_impc_ko_profile`, `search_bgee_expression`.\n- **Compounds** \u2192 ChEMBL (`chembl({action:\"compounds\"})`) for curated potency, mechanism,\n  and approved drugs. `pubchem({action:\"compound\"})` when ChEMBL misses it \u2014 then\n  bridge back to curated data with `pubchem({action:\"crossrefs\"})`.\n- **Safety** \u2192 `opentargets({action:\"safety\"})` is mechanism-based (the target);\n  `search_faers` is post-market (a specific marketed drug). EPA CTX for\n  environmental and industrial chemicals.\n\nAll of these are lightweight API calls \u2014 never spin up a sandbox for a lookup.\n\n## Hypothesis Exploration\n\nWhen the user wants to explore hypotheses, follow the scientist process\nas one continuous thought process. Do not skip phases.\n\n### 1. Orient \u2014 Understand What Exists\n- `inspect_data_profile` for the dataset's design and per-file facts.\n- Search the workspace for analysis results, DE results, QC summaries.\n- Read key files \u2014 result tables, summaries, metadata. Don't stop at search\n  results \u2014 read the files to see specific values.\n- Check run history via `inspect_run`.\n- If refining prior hypotheses, read them from conversation context.\n\n### 2. Investigate \u2014 Cross-Reference with Biology\nDelegate to the `literature_reviewer` with the genes, pathways, and\nfeatures you identified in orientation. Include fold changes, condition\nnames, and what you need to know. The reviewer systematically investigates\neach target and returns structured evidence.\n\nFor quick follow-ups on specific targets during ideation, use your\nown bio-lookup tools directly.\n\nThe goal: distinguish what's novel from what's established, and find\nbiological mechanisms that explain observed data patterns.\n\nTwo complementary tools serve hypothesis exploration: the\n`literature_reviewer` for in-domain biology evidence (used here), and\n`generate_analogy_report` for cross-domain inspiration (used in the\nIdeate step below). Treat them as a pair \u2014 biology evidence anchors\nhypotheses to reality, analogies broaden the candidate space.\n\n### 3. Ideate \u2014 Generate Candidate Hypotheses\nEach hypothesis must be:\n- **Grounded in data** \u2014 reference specific observations you verified\n  by reading actual files.\n- **Falsifiable** \u2014 a clear statement that can be confirmed or refuted.\n- **Specific** \u2014 name the genes, pathways, comparisons, expected effects.\n\n**Broaden the search space.** Before settling on a final list, consider\ncalling `generate_analogy_report` to surface cross-domain analogies for\nthe problem. Hypotheses seeded from control theory, ML, or other fields\noften map back to biology in ways that literature alone misses. Use the\nreturned analogies as candidate hypotheses (after grounding them in the\nuser's actual data) \u2014 not as the final answer, but as additional seeds\nfor the curation step.\n\n### 4. Feasibility Check\nFor each candidate, verify the data supports testing:\n- Does the required data exist?\n- Are there enough samples per group?\n- Are values in expected ranges?\n\nDrop untestable hypotheses. Flag those needing additional data.\n\n### 5. Curate \u2014 Rank and Filter\nRank by: scientific impact, testability, novelty, evidence strength,\nparsimony. Ensure hypotheses are distinguishable \u2014 they should make\ndistinct predictions. Limit to top 5-10.\n\n### Refinement Iterations\nWhen the user says \"go deeper on H2\" or \"explore the immune angle\":\n- Read all prior hypotheses from conversation context.\n- Break specified hypotheses into smaller, more specific sub-hypotheses.\n- Dig deeper \u2014 examine data you didn't check before, search more literature.\n- Return the complete updated list.\n\n### Hypothesis to Analysis\nWhen a hypothesis is ready to test, generate a plan via `generate_plan`\nwith a research question designed to test it. Present and get approval\nbefore triggering.\n\n## Responding to an Analogy Report\n\nThe UI renders `generate_analogy_report`'s result as an inline card\nautomatically. Your job is to STEER, not re-present:\n\n- 3-6 lines of plain prose. No bullets. No headers. No `show_user`.\n- Reference 2-3 analogies by their `analogyTitle` (not by re-stating\n  their content). Example: \"The *critical slowing down* angle is the\n  most actionable here \u2014 it gives you a variance-based statistic that\n  doesn't require new data.\"\n- End with one concrete steering question. Examples: \"Want me to draft\n  a plan around the DNB index?\" / \"Should we dig into the percolation\n  framing or pursue the bet-hedging entropy angle?\"\n- Never embed analogies into `generate_plan`, `execute_plan`, or any\n  workflow input. The planner and sandbox agents are unaware of\n  analogy reports by design \u2014 they're for conversation only.\n- Never call `show_user` to re-present the report. The card is the\n  presentation; your prose is the steering. Restating the analogies\n  in prose creates a duplicate rendering.\n\n## Report Creation\n\nWhen the user clearly wants a report (\"create a report of the latest run\",\n\"summarize this for the lab meeting\"), proceed without asking for\nconfirmation \u2014 state briefly what you'll build (audience, sections, format)\nin the same turn you begin.\n\nThe flow: call `plan_report` to get the report-brief schema and authoring\nrules, compose the brief from what it returns, then call `submit_report` with\nit. To revise an existing report, skip `plan_report` and call `submit_report`\nwith `modifications` + the existing `previewId` (never a fresh brief).\n\nConfirm first only when scope is genuinely ambiguous: several analyses to\nchoose from, the user is still exploring options, or the audience/format\nmatters and has not been established.\n\nDo NOT create reports unprompted. Suggest one after a run completes, or\nwhen the user asks for a summary or presentation of results.\n\n## Showing Things to the User\n\nThree display tools, each bound to a single source of truth. Pick by WHAT\nyou are referencing, not by how the output looks: `show_user` for content\nyou are inventing, `show_plan` for a stored `planId`, `show_file` for an\nexisting artifact path. Cards render in the order you emit them.\n\nChart layout is normalized for you \u2014 do not hand-tune legend, grid, axis\nrotation, or toolbox, and omit `title` from the ECharts spec.\n\n## Error Handling\n\nWhen a tool call fails, **never expose technical details**. Internal errors\n(network timeouts, pod IPs, stack traces, K8s internals) are implementation\ndetails that do not help the user.\n\nInstead:\n1. Acknowledge the failure briefly.\n2. If you can infer a user-actionable cause, mention that specifically.\n3. Offer to retry or suggest an alternative.\n4. Keep it to 2-3 sentences.\n\n## Do NOT\n\n- **Fabricate quantitative results.** Every p-value, fold change, and\n  enrichment score you cite must come from an actual file you read.\n- **Overinterpret marginal results.** A p-value of 0.04 with a small\n  effect size is not a strong finding.\n- **Synthesize from summaries alone.** When interpreting results, search\n  the workspace and read actual output files. If you cannot find the data\n  behind a claim, say so.\n- **Generate hypotheses disconnected from data.** Every hypothesis must\n  reference specific results you verified by reading files.\n- **Write just-so stories.** Hypotheses must make testable predictions.\n  If a claim fits any outcome, it is not a hypothesis \u2014 sharpen or drop it.\n- **Trigger workflows without user approval.** Always present the plan\n  and get explicit approval before starting execution.\n- **Silently violate a constraint.** A constraint in working memory is\n  binding for the rest of the analysis. If a plan or analysis choice would\n  break one \u2014 a different FDR threshold, an unpaired test on paired data \u2014\n  surface the conflict to the user. Never just proceed.\n- **Plan data exploration steps.** Data profiling runs at analysis init.\n  Never propose \"explore data structure\" or \"initial assessment\" steps.\n- **Call `run_ephemeral` multiple times for related data questions.** Each\n  call spins up a sandbox pod (~30-60s of overhead). Combine related data\n  questions into a single multi-part prompt \u2014 one call is far faster than\n  two sequential ones.\n- **Report an environment gap as permanent without checking.** \"That package\n  is not installed\" and \"that reference dataset is not here\" are facts about\n  right now, not verdicts. Before telling the user something cannot be had,\n  check whether any tool you hold can provision it, and offer that route if\n  one can. Call it impossible only after you have looked and found no path.\n\n## Guidelines\n\n- Keep responses concise and data-driven.\n- When the user's intent is ambiguous, ask a brief clarifying question.\n- Use bio-lookup tools to provide biological context for key findings,\n  but keep tool usage focused \u2014 look up the most important genes and\n  pathways, not every result.\n- When results conflict, present both sides rather than choosing one.\n- Present hypotheses in a clear, structured format with ID, claim,\n  rationale, test design, expected outcomes, and priority.\n- Suggest relevant next steps: after analysis \u2192 hypothesis exploration;\n  after hypotheses \u2192 targeted analysis to test them.\n";

package/dist/prompts/conversation.js

@@ -342,6 +342,11 @@ Instead:
   call spins up a sandbox pod (~30-60s of overhead). Combine related data
   questions into a single multi-part prompt — one call is far faster than
   two sequential ones.
+- **Report an environment gap as permanent without checking.** "That package
+  is not installed" and "that reference dataset is not here" are facts about
+  right now, not verdicts. Before telling the user something cannot be had,
+  check whether any tool you hold can provision it, and offer that route if
+  one can. Call it impossible only after you have looked and found no path.
 
 ## Guidelines
 

package/dist/prompts/planner.js

@@ -110,6 +110,19 @@ before relying on it.
   annotation rather than the run. The distinction is whether the research question
   survives without it — not whether the step does.
 
+### Available Packages
+A step can only use what is already installed in the sandbox — nothing installs at
+run time. A step that leans on an absent library is a guaranteed failure discovered
+only once the run reaches it, which is the most expensive moment to learn it.
+
+- When a step depends on a specific library, confirm it is importable before you
+  commit the step to it. Checking a handful of names is one cheap call.
+- Prefer what is present over what you would reach for by habit — an equivalent
+  installed package beats the canonical one that is not there.
+- When nothing installed can do the step's work, treat it exactly as you would an
+  absent reference: \`request_clarification\`, rather than plan a step that can
+  only report failure.
+
 ### Resource Estimation
 ${resourceEstimationSection(resourcePolicy)}
 

package/dist/tasks/data-profile.d.ts

@@ -18,6 +18,7 @@
  */
 import type { Pool } from "pg";
 import { type AuthContext, type RunSession } from "../auth/types.js";
+import type { EnvironmentStorePaths } from "../config/environment-stores.js";
 import type { RunAuthorization, RunAuthorizer } from "../execution/run-authorizer.js";
 import type { StagedInput } from "../execution/staged-input.js";
 import type { BioToolKeys } from "../tools/bio/keys.js";
@@ -29,7 +30,7 @@ import { type ResolveWorkspaceRoot } from "../workspace/paths.js";
 import { type ProfilerOutput } from "../schemas/data-profile-schemas.js";
 import { type DataProfileInputFile, type DataProfileResult } from "../state/index.js";
 /** The body's construction-time deps — closed over at registration. */
-export interface DataProfileDeps {
+export interface DataProfileDeps extends EnvironmentStorePaths {
     /** Operational logging seam; omitted falls back to no-op. */
     readonly logger?: Logger;
     readonly provider: ChatProvider;
@@ -52,18 +53,6 @@ export interface DataProfileDeps {
     readonly embedding: EmbeddingProvider;
     /** Absolute path to the skills tree (one subdirectory per skill). */
     readonly skillsDir: string;
-    /**
-     * Host path of the library store's `packages.txt`. Omit when the host mounts the
-     * store at the sandbox's own path; a host whose store is baked into the image must
-     * inject its extracted copy, or the profiler reads the inventory as unknown.
-     */
-    readonly packagesFile?: string;
-    /**
-     * Host path of the reference store. Omit only when none is provisioned: the
-     * profiler carries reference discovery, and without this it reports an installed
-     * store as absent.
-     */
-    readonly refStorePath?: string;
 }
 /**
  * Workflow input. JSON-serialisable — DBOS persists it as the workflow's

package/dist/tools/research/generate-plan.d.ts

@@ -27,8 +27,9 @@
 import type { Pool } from "pg";
 import { type ChatProvider } from "../../providers/types.js";
 import { type Tool } from "../define-tool.js";
+import type { EnvironmentStorePaths } from "../../config/environment-stores.js";
 import { type ResourcePolicy } from "../../config/resource-limits.js";
-export interface GeneratePlanDeps {
+export interface GeneratePlanDeps extends EnvironmentStorePaths {
     /** The LLM seam the planner loop runs on. */
     readonly provider: ChatProvider;
     /** Database pool — plan persistence and prior-plan loading. */
@@ -41,13 +42,6 @@ export interface GeneratePlanDeps {
      * default guidance and validation skips the ceiling check.
      */
     readonly resourcePolicy?: ResourcePolicy;
-    /**
-     * Host path of the reference store, giving the planner reference discovery.
-     * Absent, the tool reports the store as unavailable and the planner keeps
-     * planning as though nothing is guaranteed present — which is what the prompt
-     * already tells it to do.
-     */
-    readonly refStorePath?: string;
 }
 /** Build the `generate_plan` tool bound to its provider and pool. */
 export declare function createGeneratePlanTool(deps: GeneratePlanDeps): Tool;

package/dist/tools/research/generate-plan.js

@@ -32,6 +32,7 @@ import { runToTerminal } from "../../loop/run-to-terminal.js";
 import { passthroughStep } from "../../loop/run-step.js";
 import { forSubAgent, scopeResource } from "../../auth/types.js";
 import { defineTool } from "../define-tool.js";
+import { createListAvailablePackagesTool } from "../sandbox/list-available-packages.js";
 import { createListAvailableRefsTool } from "../sandbox/list-available-refs.js";
 import { createReportBlockerToolFor } from "../sandbox/report-blocker.js";
 import { DATA_PROFILE_ORIENTATION_MAX_CHARS, buildDataProfileOrientation } from "../../app/data-profile-orientation.js";
@@ -250,7 +251,10 @@ function fullyValidate(candidate, resourcePolicy) {
  * shared `holder` so the outer `execute` reads the terminal outcome after the
  * loop finishes.
  */
-function buildInnerTools(holder, persistCtx, pool, resourcePolicy, refStorePath) {
+function buildInnerTools(holder, persistCtx, pool, resourcePolicy, 
+// The two environment stores travel together as one bag rather than as a pair
+// of adjacent optional strings, which would be silently swappable at the call site.
+stores) {
     const validatePlanTool = defineTool({
         id: "validate_plan",
         description: "Dry-run a candidate plan and get back everything that is wrong with it. " +
@@ -354,12 +358,15 @@ function buildInnerTools(holder, persistCtx, pool, resourcePolicy, refStorePath)
             "incompatible with every available agent, etc.) — not for a plan you " +
             "could fix and submit.",
     });
-    // Reference discovery is non-terminal and read-only: it lets the planner check what
-    // reference data this environment actually holds before committing a step to needing
-    // it. It reads the store host-side, so no sandbox exists or is needed at plan time.
-    const listAvailableRefs = createListAvailableRefsTool(refStorePath === undefined ? {} : { refStorePath });
+    // Environment discovery is non-terminal and read-only: it lets the planner check what
+    // reference data this environment holds, and what a step will actually be able to
+    // import, before committing a step to needing either. Both read host-side, so no
+    // sandbox exists or is needed at plan time — which is the whole point, since a plan
+    // that assumes an absent package fails only once the run reaches that step.
+    const listAvailableRefs = createListAvailableRefsTool(stores.refStorePath === undefined ? {} : { refStorePath: stores.refStorePath });
+    const listAvailablePackages = createListAvailablePackagesTool(stores.packagesFile === undefined ? {} : { packagesFile: stores.packagesFile });
     const terminal = [submitPlanTool, requestClarificationTool, reportBlockerTool];
-    return { all: [validatePlanTool, listAvailableRefs, ...terminal], terminal };
+    return { all: [validatePlanTool, listAvailableRefs, listAvailablePackages, ...terminal], terminal };
 }
 /**
  * Translate the captured `PlannerOutcome` (plus any loop error) into the
@@ -491,7 +498,7 @@ export function createGeneratePlanTool(deps) {
                 analysisId,
                 parentPlanId: input.parentPlanId ?? null,
             };
-            const innerTools = buildInnerTools(holder, persistCtx, deps.pool, deps.resourcePolicy, deps.refStorePath);
+            const innerTools = buildInnerTools(holder, persistCtx, deps.pool, deps.resourcePolicy, deps);
             const planner = {
                 id: PLANNER_AGENT_ID,
                 systemPrompt: composeSystemPrompt(plannerInstructions(deps.resourcePolicy)),

package/dist/tools/sandbox/list-available-packages.d.ts

@@ -22,6 +22,7 @@
  * The file carries **names only — there are no version strings in it**, so this
  * tool reports presence and language track and cannot report a version.
  */
+import type { EnvironmentStorePaths } from "../../config/environment-stores.js";
 /** One language track of the store, in `packages.txt` section order. */
 export interface Section {
     /** The section heading verbatim, e.g. `R (CRAN)`, `Python (pip)`. */
@@ -75,16 +76,7 @@ export interface PackagesQuery {
  * is only the file read plus this call.
  */
 export declare function queryPackages(sections: readonly Section[], { names, query, language, limit }: PackagesQuery): PackagesResult;
-export interface ListAvailablePackagesDeps {
-    /**
-     * Path to the store's `packages.txt` AS THE HOST SEES IT. Defaults to the
-     * container path, which is correct only when the host mounts the same store.
-     * A host that does not — one whose store is baked into the sandbox image and
-     * never bind-mounted — must inject the path to its own extracted copy, or the
-     * read fails and every caller is told the inventory is unknown.
-     */
-    readonly packagesFile?: string;
-}
+export type ListAvailablePackagesDeps = Pick<EnvironmentStorePaths, "packagesFile">;
 /** Create the package inventory over a host-readable `packages.txt`. */
 export declare function createListAvailablePackagesTool(deps?: ListAvailablePackagesDeps): import("../define-tool.js").Tool<{
     names?: string[] | undefined;

package/dist/tools/sandbox/list-available-refs.d.ts

@@ -4,7 +4,10 @@
  * installs and user-added files alike). Narrow with `path`/`category`, filter
  * with `query`, cap with `limit`; every response carries `returned`/`total`/
  * `hasMore` and the `categories` present, so a listing is never an unbounded
- * dump. Symlinks are never followed; nothing can be downloaded at runtime.
+ * dump. Symlinks are never followed. This tool only ever READS the store: the
+ * analysis environment cannot fetch reference data, and staging more is the
+ * host's job — so an absent dataset is a fact about this moment, not a verdict
+ * that it is unobtainable.
  *
  * The store is read from the host filesystem at the embedder-supplied
  * `refStorePath` and reported at `/mnt/refs`, the container path sandboxes mount
@@ -20,14 +23,8 @@
  * only ever ENRICHES an entry — a file with no receipt and no catalog match is
  * still returned, because a user-provided store is as valid as a managed one.
  */
-export interface ListAvailableRefsDeps {
-    /**
-     * Host path of the reference store — the same bytes sandboxes see at
-     * `/mnt/refs`. Omitted (or absent on disk) means no store is provisioned,
-     * which is a normal state reported as `unavailable`, not an error.
-     */
-    readonly refStorePath?: string;
-}
+import type { EnvironmentStorePaths } from "../../config/environment-stores.js";
+export type ListAvailableRefsDeps = Pick<EnvironmentStorePaths, "refStorePath">;
 export interface ReferenceInventoryMetadata {
     readonly datasetId?: string;
     readonly version?: string;

package/dist/tools/sandbox/list-available-refs.js

@@ -4,7 +4,10 @@
  * installs and user-added files alike). Narrow with `path`/`category`, filter
  * with `query`, cap with `limit`; every response carries `returned`/`total`/
  * `hasMore` and the `categories` present, so a listing is never an unbounded
- * dump. Symlinks are never followed; nothing can be downloaded at runtime.
+ * dump. Symlinks are never followed. This tool only ever READS the store: the
+ * analysis environment cannot fetch reference data, and staging more is the
+ * host's job — so an absent dataset is a fact about this moment, not a verdict
+ * that it is unobtainable.
  *
  * The store is read from the host filesystem at the embedder-supplied
  * `refStorePath` and reported at `/mnt/refs`, the container path sandboxes mount
@@ -456,7 +459,8 @@ function collectCategories(entries) {
 }
 function renderContent(path, scan, entries) {
     if (scan.state === "unavailable")
-        return "No reference store is provisioned. Reference data cannot be downloaded at runtime; provision it through the host setup flow.";
+        return ("No reference store is provisioned. Nothing in the analysis environment can fetch reference data — the host stages it, " +
+            "so a store provisioned through the host's own path will show up on a later call.");
     if (scan.state === "not_found")
         return `Reference path does not exist: ${path}`;
     if (scan.state === "not_a_directory")
@@ -492,7 +496,8 @@ function renderContent(path, scan, entries) {
 export function createListAvailableRefsTool(deps) {
     return defineTool({
         id: "list_available_refs",
-        description: "Resolve reference data you need into a real path. Reports the reference data actually provisioned for this environment — the ONLY reference data that exists here; nothing can be downloaded at runtime. " +
+        description: "Resolve reference data you need into a real path. Reports the reference data provisioned for this environment right now — the only reference data an analysis script can open. " +
+            "Nothing inside the analysis environment reaches the network, so never write a download into a script. " +
             "Search by what the data IS, not by where you expect it: the store's directory layout is an installer detail and is not a stable interface. " +
             "Catalogued files come back with the organism, the format, and the file's internal shape (key columns, identifier space), so you can pick the right reader and the right species without opening the file first. " +
             "User-added files are returned too, with whatever labels exist — often none. Symlinks are never followed. " +
@@ -502,7 +507,9 @@ export function createListAvailableRefsTool(deps) {
             "`path` inspects one directory beneath /mnt/refs (a returned path, or store-relative) — drill in with it when a listing is truncated; " +
             '`category` is shorthand for a top-level group (e.g. "pathways", "regulatory-networks"), and the groups present come back in `categories`; ' +
             "`limit` caps the entries returned. The response carries `returned`, `total`, and `hasMore`, so truncation is never silent. " +
-            "An empty result means the data is genuinely absent — say so and proceed with what you have; do not guess a path. Provision additional files through the host setup flow.",
+            "An empty result means the dataset is absent right now — not that it is unobtainable. Say so; never guess a path, and never silently substitute a different dataset. " +
+            "The store is provisioned by the host and is NOT frozen: datasets can be added through the host's own provisioning path, and whatever is added shows up on a later call. " +
+            "So before you report a gap as permanent, check whether any tool you hold reaches that provisioning path — offer that route if one exists, and call the gap permanent only when none does.",
         inputSchema: ListAvailableRefsInputSchema,
         execute: async ({ path, category, query, limit }) => {
             // `category` is shorthand for a top-level path; an explicit `path` wins.

package/package.json

@@ -1,6 +1,6 @@
 {
     "name": "@inflexa-ai/harness",
-    "version": "0.7.0",
+    "version": "0.7.1",
     "description": "Host-agnostic bioinformatics agent harness \u2014 hand-rolled agent loop, DBOS-durable workflows, sandboxed compute.",
     "license": "Apache-2.0",
     "type": "module",