@galaxy-tool-util/cli 1.4.0 → 1.6.0

package/dist/commands/draft-extract.d.ts

@@ -0,0 +1,7 @@
+export interface DraftExtractOptions {
+    output?: string;
+    reportJson?: string | boolean;
+    format?: string;
+}
+export declare function runDraftExtract(filePath: string, opts: DraftExtractOptions): Promise<void>;
+//# sourceMappingURL=draft-extract.d.ts.map

package/dist/commands/draft-extract.d.ts.map

@@ -0,0 +1 @@
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package/dist/commands/draft-extract.js

@@ -0,0 +1,75 @@
+/**
+ * `gxwf draft-extract` — extract the concrete subset of a draft workflow.
+ *
+ * Runs `extractConcreteSubset` from @galaxy-tool-util/schema, strips
+ * `_plan_*` planning fields, and promotes `class: GalaxyWorkflowDraft` →
+ * `class: GalaxyWorkflow` on any (sub)workflow that is now fully concrete.
+ * Emits the trimmed workflow to stdout (or `-o` file) and an optional
+ * sidecar JSON report.
+ *
+ * Exit codes:
+ *   0 — input parses + extract ran (including empty-extract case)
+ *   2 — parse/read failure, native input rejected, or stdout-sink collision
+ *       (workflow → stdout AND --report-json → stdout simultaneously)
+ */
+import { writeFile } from "node:fs/promises";
+import { buildSingleDraftExtractReport, extractConcreteSubset, promoteFullyConcreteDrafts, resolveFormat, serializeWorkflow, stripPlanFields, } from "@galaxy-tool-util/schema";
+import { readWorkflowFile, writeWorkflowOutput } from "./workflow-io.js";
+import { findStdoutSinkCollision, targetsStdout } from "./report-output.js";
+export async function runDraftExtract(filePath, opts) {
+    const collision = findStdoutSinkCollision([
+        { flag: "<workflow output>", toStdout: !opts.output },
+        { flag: "--report-json", toStdout: targetsStdout(opts.reportJson) },
+    ]);
+    if (collision) {
+        console.error(collision);
+        process.exitCode = 2;
+        return;
+    }
+    const data = await readWorkflowFile(filePath);
+    if (!data) {
+        process.exitCode = 2;
+        return;
+    }
+    const format = resolveFormat(data, opts.format);
+    if (format === "native") {
+        console.error("draft-extract requires format2 — native workflows cannot be drafts");
+        process.exitCode = 2;
+        return;
+    }
+    const extract = extractConcreteSubset(data);
+    stripPlanFields(extract.workflow);
+    const promote = promoteFullyConcreteDrafts(extract.workflow);
+    const trimmed = extract.workflow != null && typeof extract.workflow === "object"
+        ? extract.workflow
+        : {};
+    const classAfter = trimmed.class === "GalaxyWorkflow" ? "GalaxyWorkflow" : "GalaxyWorkflowDraft";
+    const outputFormat = outputFormatFor(opts.output, format);
+    const serialized = serializeWorkflow(trimmed, outputFormat);
+    await writeWorkflowOutput(serialized, opts.output, "Extracted workflow");
+    if (opts.reportJson !== undefined) {
+        const report = buildSingleDraftExtractReport(filePath, opts.output ?? null, extract, promote, classAfter);
+        const json = JSON.stringify(report, null, 2);
+        const dest = opts.reportJson;
+        if (dest === true || dest === "-") {
+            console.log(json);
+        }
+        else {
+            await writeFile(dest, json + "\n", "utf-8");
+        }
+    }
+    process.exitCode = 0;
+}
+/**
+ * Resolve the workflow serialization format from -o's extension, falling
+ * back to the detected input format. `.ga` / `.json` → native (JSON);
+ * `.gxwf.yml` / other → format2 (YAML).
+ */
+function outputFormatFor(output, fallback) {
+    if (!output)
+        return fallback;
+    if (output.endsWith(".ga") || output.endsWith(".json"))
+        return "native";
+    return "format2";
+}
+//# sourceMappingURL=draft-extract.js.map

package/dist/commands/draft-extract.js.map

@@ -0,0 +1 @@
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package/dist/commands/draft-next-step.d.ts

@@ -0,0 +1,6 @@
+export interface DraftNextStepOptions {
+    format?: string;
+    outputFormat?: "json" | "markdown" | string;
+}
+export declare function runDraftNextStep(filePath: string, opts: DraftNextStepOptions): Promise<void>;
+//# sourceMappingURL=draft-next-step.d.ts.map

package/dist/commands/draft-next-step.d.ts.map

@@ -0,0 +1 @@
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package/dist/commands/draft-next-step.js

@@ -0,0 +1,49 @@
+/**
+ * `gxwf draft-next-step` — pick the next step a downstream agent should
+ * work on. Wraps `nextDraftStep` from @galaxy-tool-util/schema.
+ *
+ * Default output is JSON (the agent-loop wire format); `--output-format
+ * markdown` renders a human-glance checklist. Pure pass-through — same
+ * input → byte-identical output.
+ *
+ * Exit codes:
+ *   0 — input parses + is a (possibly non-draft) workflow document
+ *   2 — parse/read failure or format mismatch (native rejected)
+ */
+import { nextDraftStep, resolveFormat } from "@galaxy-tool-util/schema";
+import { readWorkflowFile } from "./workflow-io.js";
+export async function runDraftNextStep(filePath, opts) {
+    const data = await readWorkflowFile(filePath);
+    if (!data) {
+        process.exitCode = 2;
+        return;
+    }
+    const format = resolveFormat(data, opts.format);
+    if (format === "native") {
+        console.error("draft-next-step requires format2 — native workflows cannot be drafts");
+        process.exitCode = 2;
+        return;
+    }
+    const result = nextDraftStep(data);
+    const outputFormat = opts.outputFormat ?? "json";
+    if (outputFormat === "markdown") {
+        process.stdout.write(renderMarkdown(result));
+    }
+    else if (outputFormat === "json") {
+        console.log(JSON.stringify(result, null, 2));
+    }
+    else {
+        console.error(`unknown --output-format: ${outputFormat} (expected json or markdown)`);
+        process.exitCode = 2;
+        return;
+    }
+    process.exitCode = 0;
+}
+function renderMarkdown(result) {
+    if (!result.draft)
+        return "_No remaining draft work._\n";
+    const heading = `## Next step: \`${result.step.join(" / ")}\`\n\n`;
+    const items = result.work.map((w) => `- [ ] ${w}`).join("\n");
+    return heading + items + "\n";
+}
+//# sourceMappingURL=draft-next-step.js.map

package/dist/commands/draft-next-step.js.map

@@ -0,0 +1 @@
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package/dist/commands/draft-validate.d.ts

@@ -0,0 +1,13 @@
+import { type StrictOptions } from "./strict-options.js";
+export interface DraftValidateOptions extends StrictOptions {
+    format?: string;
+    json?: boolean;
+    reportHtml?: string | boolean;
+    reportMarkdown?: string | boolean;
+    concrete?: boolean;
+    cacheDir?: string;
+    toolState?: boolean;
+    connections?: boolean;
+}
+export declare function runDraftValidate(filePath: string, opts: DraftValidateOptions): Promise<void>;
+//# sourceMappingURL=draft-validate.d.ts.map

package/dist/commands/draft-validate.d.ts.map

@@ -0,0 +1 @@
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package/dist/commands/draft-validate.js

@@ -0,0 +1,272 @@
+/**
+ * `gxwf draft-validate` — validate a draft Galaxy workflow
+ * (class: GalaxyWorkflowDraft).
+ *
+ * Wraps `validateDraft` from @galaxy-tool-util/schema. Single-file only; the
+ * tree variant is deferred to workstream v2.
+ *
+ * With `--concrete`, additionally runs the `draft-extract` pipeline
+ * (extractConcreteSubset + stripPlanFields + promoteFullyConcreteDrafts) and
+ * runs the regular `gxwf validate` checks on the trimmed workflow:
+ *   - structural decode (always)
+ *   - --strict-structure / --strict-encoding (when the strict flags are set)
+ *   - tool-state validation (default on, --no-tool-state to skip, --cache-dir
+ *     selects the cache)
+ *   - --strict-state (when set, escalates skipped tool-state steps to errors)
+ *   - --connections (when set, runs connection-type compatibility)
+ *
+ * When the extracted subset is still a draft (not fully promoted), every
+ * concrete-stage check is skipped, not failed. The concrete pass is also
+ * skipped entirely when the draft has structural errors (the projection
+ * isn't trustworthy in that case).
+ *
+ * Exit-code differences vs. `gxwf validate`: `gxwf validate` exits 2 on
+ * strict-structure / strict-encoding failures; here, those roll into the
+ * concrete report and escalate to exit 1 — the draft itself parsed; only the
+ * projection failed.
+ *
+ * Exit codes (per workstream C):
+ *   0 — clean draft (no structure/topology/semantic errors; warnings allowed)
+ *   1 — draft validation errors (topology or semantic errors), OR --concrete
+ *       checks surfaced any failure
+ *   2 — parse failure, format mismatch, or structural decode failure
+ *       (class !== GalaxyWorkflowDraft, schema decode error)
+ */
+import { dirname } from "node:path";
+import { makeNodeToolCache } from "@galaxy-tool-util/core/node";
+import { buildSingleDraftValidationReport, checkStrictEncoding, checkStrictStructure, extractConcreteSubset, promoteFullyConcreteDrafts, resolveFormat, stripPlanFields, validateDraft, } from "@galaxy-tool-util/schema";
+import { decodeStructureErrors, validateFormat2Steps } from "./validate-workflow.js";
+import { readWorkflowFile } from "./workflow-io.js";
+import { findStdoutSinkConflict, writeReportHtml, writeReportOutput } from "./report-output.js";
+import { resolveStrictOptions } from "./strict-options.js";
+import { buildConnectionReport } from "./connection-validation.js";
+import { createDefaultResolver } from "./url-resolver.js";
+export async function runDraftValidate(filePath, opts) {
+    const conflict = findStdoutSinkConflict(opts);
+    if (conflict) {
+        console.error(conflict);
+        process.exitCode = 2;
+        return;
+    }
+    const data = await readWorkflowFile(filePath);
+    if (!data) {
+        process.exitCode = 2;
+        return;
+    }
+    const format = resolveFormat(data, opts.format);
+    if (format === "native") {
+        console.error("draft-validate requires format2 — native workflows cannot be drafts");
+        process.exitCode = 2;
+        return;
+    }
+    warnUnusedConcreteFlags(opts);
+    const result = validateDraft(data);
+    // Gate the concrete pass on draft-structure cleanliness — extractConcreteSubset
+    // early-returns the input object verbatim when class != GalaxyWorkflowDraft,
+    // and stripPlanFields would then mutate the original `data`. Skipping also
+    // avoids running validate checks on a draft we know is structurally broken.
+    const concrete = opts.concrete && result.structureErrors.length === 0
+        ? await runConcretePass(filePath, data, opts)
+        : undefined;
+    const report = buildSingleDraftValidationReport(filePath, result, concrete);
+    if (opts.json) {
+        console.log(JSON.stringify(report, null, 2));
+    }
+    else {
+        printTextReport(report, result);
+    }
+    await writeReportOutput("draft_validate.md.j2", report, opts);
+    await writeReportHtml("draft-validate", report, opts.reportHtml);
+    process.exitCode = exitCodeFor(result, concrete);
+}
+function warnUnusedConcreteFlags(opts) {
+    if (opts.concrete) {
+        if (opts.toolState === false && opts.strictState) {
+            console.error("Warning: --strict-state has no effect when tool-state validation is disabled (--no-tool-state)");
+        }
+        return;
+    }
+    const ignored = [];
+    if (opts.cacheDir)
+        ignored.push("--cache-dir");
+    if (opts.toolState === false)
+        ignored.push("--no-tool-state");
+    if (opts.connections)
+        ignored.push("--connections");
+    if (opts.strict || opts.strictStructure || opts.strictEncoding || opts.strictState) {
+        ignored.push("--strict*");
+    }
+    if (ignored.length > 0) {
+        console.error(`Warning: ${ignored.join(", ")} only apply with --concrete; ignoring`);
+    }
+}
+async function runConcretePass(filePath, data, opts) {
+    const extract = extractConcreteSubset(data);
+    stripPlanFields(extract.workflow);
+    promoteFullyConcreteDrafts(extract.workflow);
+    const trimmed = extract.workflow != null && typeof extract.workflow === "object"
+        ? extract.workflow
+        : {};
+    const class_after = trimmed.class === "GalaxyWorkflow" ? "GalaxyWorkflow" : "GalaxyWorkflowDraft";
+    // Defense-in-depth: for any draft input the gate at the call site lets
+    // through, extract+strip+promote always promotes the outer class. The only
+    // way to hit this branch is an exotic shape (e.g. inline subworkflow draft
+    // that itself fails promotion). Leaving the check here keeps the contract
+    // explicit: never decode an unpromoted subset against GalaxyWorkflowSchema.
+    if (class_after !== "GalaxyWorkflow") {
+        return {
+            class_after,
+            skipped_reason: "extracted subset is still a draft — not fully promoted",
+            structure_errors: [],
+            // ok=null (not true) — concrete validation didn't run, so we cannot
+            // claim the subset would have validated. Downstream readers must treat
+            // null as "unknown," not as a pass.
+            ok: null,
+        };
+    }
+    const strict = resolveStrictOptions(opts);
+    const report = {
+        class_after,
+        skipped_reason: null,
+        structure_errors: decodeStructureErrors(trimmed, "format2"),
+        ok: true,
+    };
+    if (strict.strictStructure) {
+        report.strict_structure_errors = checkStrictStructure(trimmed, "format2");
+    }
+    if (strict.strictEncoding) {
+        report.strict_encoding_errors = checkStrictEncoding(trimmed, "format2");
+    }
+    // Tool-state defaults to ON (matches `gxwf validate`); --no-tool-state opts out.
+    const toolStateEnabled = opts.toolState !== false;
+    if (toolStateEnabled) {
+        const cache = makeNodeToolCache({ cacheDir: opts.cacheDir });
+        await cache.index.load();
+        const expansionOpts = {
+            resolver: createDefaultResolver({ workflowDirectory: dirname(filePath) }),
+        };
+        const stepResults = await validateFormat2Steps(trimmed, cache, "", expansionOpts);
+        report.tool_state = {
+            results: stepResults,
+            summary: summarize(stepResults),
+        };
+        if (strict.strictState) {
+            const skipped = stepResults.filter((r) => r.status !== "ok" && r.status !== "fail");
+            report.strict_state_errors = skipped.map((r) => `${r.step} (${r.tool_id ?? "?"}): skipped (${r.status})`);
+        }
+        if (opts.connections) {
+            report.connection_report = await buildConnectionReport(trimmed, cache);
+        }
+    }
+    else if (opts.connections) {
+        // --connections without tool-state still needs a cache to look up tools.
+        const cache = makeNodeToolCache({ cacheDir: opts.cacheDir });
+        await cache.index.load();
+        report.connection_report = await buildConnectionReport(trimmed, cache);
+    }
+    report.ok = isConcreteOk(report);
+    return report;
+}
+function summarize(results) {
+    let ok = 0;
+    let fail = 0;
+    let skip = 0;
+    for (const r of results) {
+        if (r.status === "ok")
+            ok++;
+        else if (r.status === "fail")
+            fail++;
+        else
+            skip++;
+    }
+    return { ok, fail, skip };
+}
+function isConcreteOk(c) {
+    if (c.skipped_reason !== null)
+        return null;
+    if (c.structure_errors.length > 0)
+        return false;
+    if (c.strict_structure_errors && c.strict_structure_errors.length > 0)
+        return false;
+    if (c.strict_encoding_errors && c.strict_encoding_errors.length > 0)
+        return false;
+    if (c.strict_state_errors && c.strict_state_errors.length > 0)
+        return false;
+    if (c.tool_state && c.tool_state.summary.fail > 0)
+        return false;
+    if (c.connection_report && !c.connection_report.valid)
+        return false;
+    return true;
+}
+function exitCodeFor(result, concrete) {
+    if (result.structureErrors.length > 0)
+        return 2;
+    if (result.topologyErrors.length > 0 || result.semanticErrors.length > 0)
+        return 1;
+    // Only explicit `false` escalates — `null` (skipped) is informational.
+    if (concrete && concrete.ok === false)
+        return 1;
+    return 0;
+}
+function printTextReport(report, result) {
+    console.log(`Draft validation: ${report.workflow}`);
+    console.log(`  ${report.summary}`);
+    printBucket("Structure errors", result.structureErrors);
+    printBucket("Topology errors", result.topologyErrors);
+    printBucket("Semantic errors", result.semanticErrors);
+    printBucket("Warnings", result.warnings);
+    const survey = report.survey;
+    console.log(`  Survey: ${survey.todo_count} TODO sentinel${survey.todo_count === 1 ? "" : "s"}` +
+        ` across ${survey.todo_paths.length} step path${survey.todo_paths.length === 1 ? "" : "s"};` +
+        ` ${survey.plan_step_paths.length} step${survey.plan_step_paths.length === 1 ? "" : "s"} with _plan_* fields`);
+    if (report.concrete)
+        printConcrete(report.concrete);
+}
+function printConcrete(concrete) {
+    if (concrete.skipped_reason) {
+        console.log(`  Concrete: SKIPPED (${concrete.skipped_reason})`);
+        return;
+    }
+    console.log(`  Concrete: ${concrete.ok === true ? "OK" : "FAIL"}`);
+    printList("    Structure errors", concrete.structure_errors);
+    if (concrete.strict_structure_errors)
+        printList("    Strict-structure errors", concrete.strict_structure_errors);
+    if (concrete.strict_encoding_errors)
+        printList("    Strict-encoding errors", concrete.strict_encoding_errors);
+    if (concrete.strict_state_errors)
+        printList("    Strict-state errors", concrete.strict_state_errors);
+    if (concrete.tool_state) {
+        const { ok, fail, skip } = concrete.tool_state.summary;
+        console.log(`    Tool state: ${ok} ok, ${fail} fail, ${skip} skip`);
+        for (const r of concrete.tool_state.results) {
+            if (r.status === "ok")
+                continue;
+            const tag = r.tool_id ? `${r.step} (${r.tool_id})` : r.step;
+            console.log(`      ${tag} [${r.status}]`);
+            for (const e of r.errors)
+                console.log(`        ${e}`);
+        }
+    }
+    if (concrete.connection_report) {
+        const cr = concrete.connection_report;
+        const { ok = 0, invalid = 0, skip = 0 } = cr.summary;
+        console.log(`    Connections: ${cr.valid ? "OK" : "INVALID"} — ${ok} ok, ${invalid} invalid, ${skip} skip`);
+    }
+}
+function printList(label, lines) {
+    if (lines.length === 0)
+        return;
+    console.log(`${label} (${lines.length}):`);
+    for (const line of lines)
+        console.log(`      ${line}`);
+}
+function printBucket(label, diagnostics) {
+    if (diagnostics.length === 0)
+        return;
+    console.log(`  ${label} (${diagnostics.length}):`);
+    for (const d of diagnostics) {
+        const where = d.path.length === 0 ? "<workflow>" : d.path.join("/");
+        console.log(`    ${where}: ${d.message}`);
+    }
+}
+//# sourceMappingURL=draft-validate.js.map

package/dist/commands/draft-validate.js.map

@@ -0,0 +1 @@
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package/dist/commands/report-output.d.ts

@@ -1,4 +1,4 @@
-export type ReportType = "validate" | "lint" | "clean" | "validate-tree" | "lint-tree" | "clean-tree" | "roundtrip-tree";
+export type ReportType = "validate" | "lint" | "clean" | "draft-validate" | "validate-tree" | "lint-tree" | "clean-tree" | "roundtrip-tree";
 export interface ReportOutputOptions {
     /**
      * Path to write Markdown report to. Commander sets this to `true` (boolean)
@@ -9,6 +9,32 @@ export interface ReportOutputOptions {
     /** Same semantics as reportMarkdown but for HTML output. */
     reportHtml?: string | boolean;
 }
+/** True if dest is unset to a filename and would write to stdout. */
+declare function targetsStdout(dest: string | boolean | undefined): boolean;
+/**
+ * If more than one sink in `candidates` would write to stdout, return an
+ * error message naming the conflicting flags. Otherwise null.
+ *
+ * Generalizes `findStdoutSinkConflict` for commands whose stdout sinks
+ * aren't drawn from the standard `--json` / `--report-{html,markdown}`
+ * set (e.g. `draft-extract` writes the trimmed workflow to stdout by
+ * default + `--report-json` may also target stdout).
+ */
+export declare function findStdoutSinkCollision(candidates: Array<{
+    flag: string;
+    toStdout: boolean;
+}>): string | null;
+/**
+ * If more than one report sink (JSON + rendered reports) would write to
+ * stdout, return an error message describing the conflict. Otherwise null.
+ */
+export declare function findStdoutSinkConflict(opts: {
+    json?: boolean;
+    reportHtml?: string | boolean;
+    reportMarkdown?: string | boolean;
+}): string | null;
+/** Re-export for command handlers that need their own collision-detection sites. */
+export { targetsStdout };
 /**
  * Render and write report output if --report-markdown / --report-html flags
  * were passed. Both can be specified simultaneously.

package/dist/commands/report-output.d.ts.map

@@ -1 +1 @@
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package/dist/commands/report-output.js

@@ -7,6 +7,38 @@ import { renderReport } from "../workflow/report-templates.js";
 // Bump when a new shell version with user-visible changes is released to npm.
 const SHELL_CDN_VERSION = "0.1.0";
 const SHELL_CDN_BASE = `https://cdn.jsdelivr.net/npm/@galaxy-tool-util/gxwf-report-shell@${SHELL_CDN_VERSION}/dist`;
+/** True if dest is unset to a filename and would write to stdout. */
+function targetsStdout(dest) {
+    return dest === true || dest === "-";
+}
+/**
+ * If more than one sink in `candidates` would write to stdout, return an
+ * error message naming the conflicting flags. Otherwise null.
+ *
+ * Generalizes `findStdoutSinkConflict` for commands whose stdout sinks
+ * aren't drawn from the standard `--json` / `--report-{html,markdown}`
+ * set (e.g. `draft-extract` writes the trimmed workflow to stdout by
+ * default + `--report-json` may also target stdout).
+ */
+export function findStdoutSinkCollision(candidates) {
+    const sinks = candidates.filter((c) => c.toStdout).map((c) => c.flag);
+    if (sinks.length < 2)
+        return null;
+    return `cannot write ${sinks.join(" + ")} to stdout simultaneously — pick one, or redirect a report to a file`;
+}
+/**
+ * If more than one report sink (JSON + rendered reports) would write to
+ * stdout, return an error message describing the conflict. Otherwise null.
+ */
+export function findStdoutSinkConflict(opts) {
+    return findStdoutSinkCollision([
+        { flag: "--json", toStdout: !!opts.json },
+        { flag: "--report-html", toStdout: targetsStdout(opts.reportHtml) },
+        { flag: "--report-markdown", toStdout: targetsStdout(opts.reportMarkdown) },
+    ]);
+}
+/** Re-export for command handlers that need their own collision-detection sites. */
+export { targetsStdout };
 /**
  * Render and write report output if --report-markdown / --report-html flags
  * were passed. Both can be specified simultaneously.

package/dist/commands/report-output.js.map

@@ -1 +1 @@
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package/dist/commands/validate-tool-source-tree.d.ts

@@ -0,0 +1,28 @@
+/**
+ * ``gxwf validate-tool-source-tree`` — batch-validate every user-defined tool
+ * source YAML under a directory. Discovery parses each candidate YAML and
+ * checks for ``class: GalaxyUserTool`` / ``class: GalaxyTool`` rather than
+ * relying on a filename suffix (UDTs don't have an established convention).
+ */
+import { type UserToolSourceDiagnostic } from "@galaxy-tool-util/schema";
+export interface ValidateToolSourceTreeOptions {
+    json?: boolean;
+    schemaOnly?: boolean;
+}
+export interface ToolSourceTreeFileReport {
+    path: string;
+    valid: boolean;
+    errors: UserToolSourceDiagnostic[];
+}
+export interface ValidateToolSourceTreeReport {
+    root: string;
+    files: ToolSourceTreeFileReport[];
+    summary: {
+        total: number;
+        ok: number;
+        fail: number;
+        error: number;
+    };
+}
+export declare function runValidateToolSourceTree(dir: string, opts?: ValidateToolSourceTreeOptions): Promise<void>;
+//# sourceMappingURL=validate-tool-source-tree.d.ts.map

package/dist/commands/validate-tool-source-tree.d.ts.map

@@ -0,0 +1 @@
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