npm - helixlife-expert-cli - Versions diffs - 0.3.0 → 0.3.1 - Mend

helixlife-expert-cli 0.3.0 → 0.3.1

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Files changed (111) hide show

package/cli/dist/modules/meta/writing.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"writing.d.ts","sourceRoot":"","sources":["../../../src/modules/meta/writing.ts"],"names":[],"mappings":"~~AAEA~~,OAAO,EAA0G,KAAK,YAAY,EAAE,MAAM,qBAAqB,CAAC;AAIhK,OAAO,KAAK,EAAsB,gBAAgB,EAAmB,MAAM,YAAY,CAAC;AAmBxF,MAAM,WAAW,sBAAsB;IACrC,UAAU,EAAE,MAAM,CAAC;IACnB,MAAM,CAAC,EAAE,YAAY,CAAC;IACtB,UAAU,CAAC,EAAE,MAAM,CAAC;CACrB;AAED,MAAM,WAAW,mBAAoB,SAAQ,sBAAsB;IACjE,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB;AAED,MAAM,WAAW,oBAAqB,SAAQ,sBAAsB;IAClE,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,SAAS,CAAC,EAAE,MAAM,CAAC;CACpB;AAED,MAAM,WAAW,0BAA2B,SAAQ,oBAAoB;IACtE,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,cAAc,CAAC,EAAE,MAAM,CAAC;IACxB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB;AAED,MAAM,WAAW,4BAA6B,SAAQ,sBAAsB;IAC1E,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,cAAc,CAAC,EAAE,MAAM,CAAC;IACxB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,YAAY,CAAC,EAAE,MAAM,CAAC;CACvB;AAED,MAAM,WAAW,kBAAmB,SAAQ,sBAAsB;IAChE,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB;AAED,MAAM,WAAW,oBAAqB,SAAQ,kBAAkB;IAC9D,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB;AAED,MAAM,WAAW,kBAAmB,SAAQ,kBAAkB;IAC5D,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAED,MAAM,WAAW,qBAAsB,SAAQ,kBAAkB;IAC/D,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,YAAY,CAAC,EAAE,MAAM,CAAC;CACvB;AAED,MAAM,WAAW,qBAAqB;IACpC,QAAQ,EAAE,MAAM,CAAC;IACjB,MAAM,EAAE,MAAM,CAAC;IACf,QAAQ,EAAE,MAAM,CAAC;IACjB,MAAM,EAAE,MAAM,CAAC;IACf,KAAK,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;IAC/B,MAAM,EAAE,OAAO,CAAC;IAChB,IAAI,EAAE,gBAAgB,CAAC;CACxB;AAED,MAAM,WAAW,uBAAuB;IACtC,QAAQ,EAAE,MAAM,CAAC;IACjB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,IAAI,EAAE,OAAO,CAAC;CACf;~~AA44BD~~,wBAAsB,sBAAsB,CAAC,OAAO,EAAE,mBAAmB,GAAG,OAAO,CAAC,IAAI,CAAC,CAyBxF;AAED,wBAAsB,mBAAmB,CAAC,OAAO,EAAE,kBAAkB,GAAG,OAAO,CAAC,IAAI,CAAC,CAoBpF;AAED,wBAAsB,qBAAqB,CAAC,OAAO,EAAE,kBAAkB,GAAG,OAAO,CAAC,IAAI,CAAC,CAyBtF;AAED;;GAEG;AACH,wBAAsB,sBAAsB,CAAC,OAAO,EAAE,kBAAkB,GAAG,OAAO,CAAC,IAAI,CAAC,CAwBvF;AAED,wBAAsB,sBAAsB,CAAC,OAAO,EAAE,0BAA0B,GAAG,OAAO,CAAC,IAAI,CAAC,CAkC/F;AAED,wBAAsB,mBAAmB,CAAC,OAAO,EAAE,oBAAoB,GAAG,OAAO,CAAC,IAAI,CAAC,CAuBtF;AAED,wBAAsB,qBAAqB,CAAC,OAAO,EAAE,oBAAoB,GAAG,OAAO,CAAC,IAAI,CAAC,CA4BxF;AAED;;GAEG;AACH,wBAAsB,sBAAsB,CAAC,OAAO,EAAE,kBAAkB,GAAG,OAAO,CAAC,IAAI,CAAC,CA2BvF;AAED,wBAAsB,wBAAwB,CAAC,OAAO,EAAE,4BAA4B,GAAG,OAAO,CAAC,IAAI,CAAC,CAiDnG;AAED,wBAAsB,qBAAqB,CAAC,OAAO,EAAE,kBAAkB,GAAG,OAAO,CAAC,IAAI,CAAC,CAyCtF;AAED,wBAAsB,uBAAuB,CAAC,OAAO,EAAE,kBAAkB,GAAG,OAAO,CAAC,IAAI,CAAC,CAExF;AAED,wBAAsB,wBAAwB,CAAC,OAAO,EAAE,qBAAqB,GAAG,OAAO,CAAC,IAAI,CAAC,CAa5F"}
1	+ {"version":3,"file":"writing.d.ts","sourceRoot":"","sources":["../../../src/modules/meta/writing.ts"],"names":[],"mappings":"AAGA,OAAO,EAA0G,KAAK,YAAY,EAAE,MAAM,qBAAqB,CAAC;AAIhK,OAAO,KAAK,EAAsB,gBAAgB,EAAmB,MAAM,YAAY,CAAC;AAmBxF,MAAM,WAAW,sBAAsB;IACrC,UAAU,EAAE,MAAM,CAAC;IACnB,MAAM,CAAC,EAAE,YAAY,CAAC;IACtB,UAAU,CAAC,EAAE,MAAM,CAAC;CACrB;AAED,MAAM,WAAW,mBAAoB,SAAQ,sBAAsB;IACjE,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB;AAED,MAAM,WAAW,oBAAqB,SAAQ,sBAAsB;IAClE,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,SAAS,CAAC,EAAE,MAAM,CAAC;CACpB;AAED,MAAM,WAAW,0BAA2B,SAAQ,oBAAoB;IACtE,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,cAAc,CAAC,EAAE,MAAM,CAAC;IACxB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB;AAED,MAAM,WAAW,4BAA6B,SAAQ,sBAAsB;IAC1E,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,cAAc,CAAC,EAAE,MAAM,CAAC;IACxB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,YAAY,CAAC,EAAE,MAAM,CAAC;CACvB;AAED,MAAM,WAAW,kBAAmB,SAAQ,sBAAsB;IAChE,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB;AAED,MAAM,WAAW,oBAAqB,SAAQ,kBAAkB;IAC9D,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB;AAED,MAAM,WAAW,kBAAmB,SAAQ,kBAAkB;IAC5D,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAED,MAAM,WAAW,qBAAsB,SAAQ,kBAAkB;IAC/D,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,YAAY,CAAC,EAAE,MAAM,CAAC;CACvB;AAED,MAAM,WAAW,qBAAqB;IACpC,QAAQ,EAAE,MAAM,CAAC;IACjB,MAAM,EAAE,MAAM,CAAC;IACf,QAAQ,EAAE,MAAM,CAAC;IACjB,MAAM,EAAE,MAAM,CAAC;IACf,KAAK,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;IAC/B,MAAM,EAAE,OAAO,CAAC;IAChB,IAAI,EAAE,gBAAgB,CAAC;CACxB;AAED,MAAM,WAAW,uBAAuB;IACtC,QAAQ,EAAE,MAAM,CAAC;IACjB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,IAAI,EAAE,OAAO,CAAC;CACf;AAk5BD,wBAAsB,sBAAsB,CAAC,OAAO,EAAE,mBAAmB,GAAG,OAAO,CAAC,IAAI,CAAC,CAyBxF;AAED,wBAAsB,mBAAmB,CAAC,OAAO,EAAE,kBAAkB,GAAG,OAAO,CAAC,IAAI,CAAC,CAoBpF;AAED,wBAAsB,qBAAqB,CAAC,OAAO,EAAE,kBAAkB,GAAG,OAAO,CAAC,IAAI,CAAC,CAyBtF;AAED;;GAEG;AACH,wBAAsB,sBAAsB,CAAC,OAAO,EAAE,kBAAkB,GAAG,OAAO,CAAC,IAAI,CAAC,CAwBvF;AAED,wBAAsB,sBAAsB,CAAC,OAAO,EAAE,0BAA0B,GAAG,OAAO,CAAC,IAAI,CAAC,CAkC/F;AAED,wBAAsB,mBAAmB,CAAC,OAAO,EAAE,oBAAoB,GAAG,OAAO,CAAC,IAAI,CAAC,CAuBtF;AAED,wBAAsB,qBAAqB,CAAC,OAAO,EAAE,oBAAoB,GAAG,OAAO,CAAC,IAAI,CAAC,CA4BxF;AAED;;GAEG;AACH,wBAAsB,sBAAsB,CAAC,OAAO,EAAE,kBAAkB,GAAG,OAAO,CAAC,IAAI,CAAC,CA2BvF;AAED,wBAAsB,wBAAwB,CAAC,OAAO,EAAE,4BAA4B,GAAG,OAAO,CAAC,IAAI,CAAC,CAiDnG;AAED,wBAAsB,qBAAqB,CAAC,OAAO,EAAE,kBAAkB,GAAG,OAAO,CAAC,IAAI,CAAC,CAyCtF;AAED,wBAAsB,uBAAuB,CAAC,OAAO,EAAE,kBAAkB,GAAG,OAAO,CAAC,IAAI,CAAC,CAExF;AAED,wBAAsB,wBAAwB,CAAC,OAAO,EAAE,qBAAqB,GAAG,OAAO,CAAC,IAAI,CAAC,CAa5F"}

package/cli/dist/modules/meta/writing.js CHANGED Viewed

@@ -1,5 +1,6 @@
 import { mkdir, readFile, stat, writeFile } from "node:fs/promises";
-import { basename, dirname, extname, join, resolve } from "node:path";
+import { resolveUserPath } from "../../core/paths.js";
+import { basename, dirname, extname, join } from "node:path";
 import { ApiClient, createStderrProgress, helixlifeError, helixlifeErrorCode, printOutput, renderListAsMarkdown } from "../../core/index.js";
 import { requestMeta } from "./api.js";
 import { META_API_PREFIX, META_FULLTEXT_WAIT_HINT } from "./constants.js";
@@ -81,14 +82,14 @@ function parseJsonObject(raw, optionName) {
 }
 async function parseJsonObjectInput(raw, filePath) {
     if (filePath?.trim()) {
-        const content = await readFile(filePath.trim(), "utf8");
+        const content = await readFile(resolveUserPath(filePath.trim()), "utf8");
         return parseJsonObject(content, "--input-file");
     }
     return parseJsonObject(raw, "--input-json");
 }
 async function readTextInput(text, filePath) {
     if (filePath?.trim()) {
-        return readFile(filePath.trim(), "utf8");
+        return readFile(resolveUserPath(filePath.trim()), "utf8");
     }
     if (text === undefined) {
         throw new helixlifeError(helixlifeErrorCode.INVALID_ARGUMENT, "缺少 --text 或 --text-file");
@@ -609,9 +610,12 @@ async function exportFullText(options) {
     const responseFilename = options.filename?.trim()
         ? requestFilename
         : normalizeExportFilename(result.filename ?? requestFilename, exportFormat);
-    const outputTarget = options.output?.trim();
+    const rawOutputTarget = options.output?.trim();
+    const outputTarget = rawOutputTarget
+        ? resolveUserPath(rawOutputTarget) + (/[\\/]$/.test(rawOutputTarget) ? "/" : "")
+        : undefined;
     const outputStat = outputTarget ? await stat(outputTarget).catch(() => undefined) : undefined;
-    const outputPath = resolve(!outputTarget
+    const outputPath = resolveUserPath(!outputTarget
         ? responseFilename
         : outputStat?.isDirectory() || outputTarget.endsWith("/") || outputTarget.endsWith("\\")
             ? join(outputTarget, responseFilename)
@@ -681,7 +685,10 @@ async function writeWritingMarkdown(kind, text, output) {
         : kind === "result"
             ? "结果.md"
             : "全文.md";
-    const target = output?.trim();
+    const rawTarget = output?.trim();
+    const target = rawTarget
+        ? resolveUserPath(rawTarget) + (/[\\/]$/.test(rawTarget) ? "/" : "")
+        : undefined;
     const targetStat = target ? await stat(target).catch(() => undefined) : undefined;
     const requestedPath = !target
         ? join(".", filename)
@@ -692,7 +699,7 @@ async function writeWritingMarkdown(kind, text, output) {
                 : extname(target)
                     ? join(dirname(target), filename)
                     : join(target, filename);
-    const outputPath = resolve(requestedPath);
+    const outputPath = resolveUserPath(requestedPath);
     await mkdir(dirname(outputPath), { recursive: true });
     const buffer = Buffer.from(text, "utf8");
     await writeFile(outputPath, buffer);

package/cli/dist/modules/meta/writing.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/cli/dist/modules/proposal/commands/bioinfo-run.d.ts CHANGED Viewed

@@ -2,5 +2,6 @@ import type { OutputFormat } from "../../../core/index.js";
 export declare function runBioinfoWorkflow(options: {
     inputsFile: string;
     format: OutputFormat;
+    fresh?: boolean;
 }): Promise<void>;
 //# sourceMappingURL=bioinfo-run.d.ts.map

package/cli/dist/modules/proposal/commands/bioinfo-run.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"bioinfo-run.d.ts","sourceRoot":"","sources":["../../../../src/modules/proposal/commands/bioinfo-run.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,wBAAwB,CAAC;AAI3D,wBAAsB,kBAAkB,CAAC,OAAO,EAAE;IAChD,UAAU,EAAE,MAAM,CAAC;IACnB,MAAM,EAAE,YAAY,CAAC;IACrB,KAAK,CAAC,EAAE,OAAO,CAAC;CACjB,GAAG,OAAO,CAAC,IAAI,CAAC,CAOhB"}

package/cli/dist/modules/proposal/commands/bioinfo-run.js CHANGED Viewed

@@ -5,6 +5,7 @@ export async function runBioinfoWorkflow(options) {
         workflow: PROPOSAL_BIOINFO_WORKFLOW,
         inputsFile: options.inputsFile,
         format: options.format,
+        fresh: options.fresh,
     });
 }
 //# sourceMappingURL=bioinfo-run.js.map

package/cli/dist/modules/proposal/commands/bioinfo-run.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"bioinfo-run.js","sourceRoot":"","sources":["../../../../src/modules/proposal/commands/bioinfo-run.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,cAAc,EAAE,MAAM,oCAAoC,CAAC;AACpE,OAAO,EAAE,yBAAyB,EAAE,MAAM,iBAAiB,CAAC;AAE5D,MAAM,CAAC,KAAK,UAAU,kBAAkB,CAAC,OAIxC;IACC,MAAM,cAAc,CAAC;QACnB,QAAQ,EAAE,yBAAyB;QACnC,UAAU,EAAE,OAAO,CAAC,UAAU;QAC9B,MAAM,EAAE,OAAO,CAAC,MAAM;QACtB,KAAK,EAAE,OAAO,CAAC,KAAK;KACrB,CAAC,CAAC;AACL,CAAC"}

package/cli/dist/modules/proposal/commands/clinical-run.d.ts CHANGED Viewed

@@ -3,5 +3,6 @@ export declare function runClinicalWorkflow(options: {
     source: string;
     inputsFile: string;
     format: OutputFormat;
+    fresh?: boolean;
 }): Promise<void>;
 //# sourceMappingURL=clinical-run.d.ts.map

package/cli/dist/modules/proposal/commands/clinical-run.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"clinical-run.d.ts","sourceRoot":"","sources":["../../../../src/modules/proposal/commands/clinical-run.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,wBAAwB,CAAC;AAI3D,wBAAsB,mBAAmB,CAAC,OAAO,EAAE;IACjD,MAAM,EAAE,MAAM,CAAC;IACf,UAAU,EAAE,MAAM,CAAC;IACnB,MAAM,EAAE,YAAY,CAAC;IACrB,KAAK,CAAC,EAAE,OAAO,CAAC;CACjB,GAAG,OAAO,CAAC,IAAI,CAAC,CAOhB"}

package/cli/dist/modules/proposal/commands/clinical-run.js CHANGED Viewed

@@ -5,6 +5,7 @@ export async function runClinicalWorkflow(options) {
         workflow: parseClinicalWorkflow(options.source),
         inputsFile: options.inputsFile,
         format: options.format,
+        fresh: options.fresh,
     });
 }
 //# sourceMappingURL=clinical-run.js.map

package/cli/dist/modules/proposal/commands/clinical-run.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"clinical-run.js","sourceRoot":"","sources":["../../../../src/modules/proposal/commands/clinical-run.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,cAAc,EAAE,MAAM,oCAAoC,CAAC;AACpE,OAAO,EAAE,qBAAqB,EAAE,MAAM,iBAAiB,CAAC;AAExD,MAAM,CAAC,KAAK,UAAU,mBAAmB,CAAC,OAKzC;IACC,MAAM,cAAc,CAAC;QACnB,QAAQ,EAAE,qBAAqB,CAAC,OAAO,CAAC,MAAM,CAAC;QAC/C,UAAU,EAAE,OAAO,CAAC,UAAU;QAC9B,MAAM,EAAE,OAAO,CAAC,MAAM;QACtB,KAAK,EAAE,OAAO,CAAC,KAAK;KACrB,CAAC,CAAC;AACL,CAAC"}

package/cli/dist/modules/proposal/index.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/modules/proposal/index.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;~~AAqBzC~~,wBAAgB,wBAAwB,CAAC,OAAO,EAAE,OAAO,GAAG,IAAI,~~CA4F~~/D"}
1	+ {"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/modules/proposal/index.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAsBzC,wBAAgB,wBAAwB,CAAC,OAAO,EAAE,OAAO,GAAG,IAAI,CAuG/D"}

package/cli/dist/modules/proposal/index.js CHANGED Viewed

@@ -5,6 +5,7 @@ import { runClinicalWorkflowParams } from "./commands/clinical-params.js";
 import { runClinicalWorkflow } from "./commands/clinical-run.js";
 import { runBioinfoWorkflowParams } from "./commands/bioinfo-params.js";
 import { runBioinfoWorkflow } from "./commands/bioinfo-run.js";
+import { WORKFLOW_RUN_FRESH_HINT as FRESH_HINT } from "../shared/workflow-app/index.js";
 const CLINICAL_SOURCE_HINT = `工作流：${PROPOSAL_CLINICAL_SOURCES.join(" | ")}`;
 // 注册课题方案专家命名空间。
 // 基础研究经外部 newidea CLI（npm: @helixlife-ai/newidea）异步执行；
@@ -63,11 +64,13 @@ export function registerProposalCommands(program) {
         .requiredOption("--source <source>", CLINICAL_SOURCE_HINT)
         .requiredOption("--inputs-file <path>", "JSON 文件 {字段名: 值}")
         .option("--format <format>", "输出格式：markdown | json", "markdown")
+        .option("--fresh", FRESH_HINT)
         .action(async (opts) => {
         await runClinicalWorkflow({
             source: opts.source,
             inputsFile: opts.inputsFile,
             format: parseOutputFormat(opts.format),
+            fresh: opts.fresh,
         });
     });
     const bioinfo = proposal
@@ -85,10 +88,12 @@ export function registerProposalCommands(program) {
         .description("按填好的参数生成生信分析方案")
         .requiredOption("--inputs-file <path>", "JSON 文件 {字段名: 值}")
         .option("--format <format>", "输出格式：markdown | json", "markdown")
+        .option("--fresh", FRESH_HINT)
         .action(async (opts) => {
         await runBioinfoWorkflow({
             inputsFile: opts.inputsFile,
             format: parseOutputFormat(opts.format),
+            fresh: opts.fresh,
         });
     });
 }

package/cli/dist/modules/proposal/index.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/cli/dist/modules/sci/article-cache.d.ts CHANGED Viewed

@@ -7,7 +7,7 @@ export interface SciArticleCachePayload {
     references: string[];
     workflowRunId?: string;
 }
-export declare function __setSciArticleCacheDirForTesting(dir: string): void;
+export declare function __setSciArticleCacheDirForTesting(dir: string | null): void;
 export declare function getSciArticleCacheDir(): string;
 export declare function resolveSciArticleCachePath(orderId: string): string;
 /**

package/cli/dist/modules/sci/article-cache.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/cli/dist/modules/sci/article-cache.js CHANGED Viewed

@@ -1,36 +1,36 @@
 /**
- * SCI 全文系统临时目录缓存
+ * SCI 全文跨进程缓存
  *
  * 设计目标：跨 CLI 进程传递步骤② 生成的全文 Markdown，步骤③ 成功后立即清理。
  *
- * 与 JOVA 综述工作台 helixlife-jova-cache/ 对齐：
- *   - 存储路径为系统临时目录 helixlife-sci-cache/（不污染用户目录）
- *   - 删除时机为步骤③ docx/md 成功后 pop，而非持久化到用户目录
+ * 存储路径为 helixlife 状态目录 sci/（Open-Science 下为会话 handoff，否则 ~/.config/helixlife/cache）；
+ * 删除时机为步骤③ docx/md 成功后 pop。
  *
  * 跨进程可见性：helixlife 每条命令是独立 Node 进程，必须落盘才能跨进程复用。
  */
 import { randomBytes } from "node:crypto";
 import { chmod, mkdir, readFile, rename, rm, writeFile, } from "node:fs/promises";
-import { tmpdir } from "node:os";
 import { join } from "node:path";
+import { getHelixlifeStateDir, pruneStaleStateFiles, } from "../../core/index.js";
 import { isCompleteSciArticleMarkdown } from "./article-validate.js";
-// 系统临时目录：mac/linux /tmp/helixlife-sci-cache/；Windows %TEMP%\helixlife-sci-cache\
-let CACHE_DIR = join(tmpdir(), "helixlife-sci-cache");
+let CACHE_DIR_OVERRIDE = null;
 const CACHE_FILE_PREFIX = "article-";
 const CACHE_FILE_EXT = ".json";
-// 仅供单元测试：覆盖缓存目录，避免污染真实系统临时目录
+// 仅供单元测试：覆盖缓存目录，避免污染真实状态目录
 export function __setSciArticleCacheDirForTesting(dir) {
-    CACHE_DIR = dir;
+    CACHE_DIR_OVERRIDE = dir;
 }
 export function getSciArticleCacheDir() {
-    return CACHE_DIR;
+    return CACHE_DIR_OVERRIDE ?? getHelixlifeStateDir("sci");
 }
 // 根据 orderId 计算缓存文件路径（供 E2E / 诊断使用）
 export function resolveSciArticleCachePath(orderId) {
-    return join(CACHE_DIR, `${CACHE_FILE_PREFIX}${sanitizeOrderId(orderId)}${CACHE_FILE_EXT}`);
+    return join(getSciArticleCacheDir(), `${CACHE_FILE_PREFIX}${sanitizeOrderId(orderId)}${CACHE_FILE_EXT}`);
 }
 async function ensureCacheDir() {
-    await mkdir(CACHE_DIR, { recursive: true });
+    const dir = getSciArticleCacheDir();
+    await mkdir(dir, { recursive: true });
+    await pruneStaleStateFiles(dir);
 }
 // 安全过滤 orderId，避免路径穿越
 function sanitizeOrderId(orderId) {

package/cli/dist/modules/sci/article-cache.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/cli/dist/modules/sci/commands/article-download.js CHANGED Viewed

@@ -1,7 +1,7 @@
 // SCI 全文导出（Step3）：命中步骤② 系统临时目录缓存 → 追加参考文献 → 输出 MD + Word
-import { readFile, writeFile } from "node:fs/promises";
-import { extname, join } from "node:path";
-import { ApiClient, getDefaultNewideaBaseUrl, helixlifeError, helixlifeErrorCode, getUserDownloadsDir, printOutput, resolveUserPath, sanitizeFilename, } from "../../../core/index.js";
+import { mkdir, readFile, writeFile } from "node:fs/promises";
+import { dirname, extname, join } from "node:path";
+import { ApiClient, getDefaultNewideaBaseUrl, helixlifeError, helixlifeErrorCode, getHelixlifeOutputDir, printOutput, resolveUserPath, sanitizeFilename, } from "../../../core/index.js";
 import { SCI_ARTICLE_CONTENT_PRODUCER, SCI_DOCX_CONVERT_API_PATH, } from "../constants.js";
 import { loadSciArticleCache, popSciArticleCache } from "../article-cache.js";
 const DEFAULT_SCI_ARTICLE_TITLE = "未命名";
@@ -193,7 +193,7 @@ export function resolveArticleDownloadPath(outputOption, articleTitle) {
         }
         return join(resolved, safeName);
     }
-    return join(getUserDownloadsDir(), safeName);
+    return join(getHelixlifeOutputDir(), safeName);
 }
 // 由 docx 路径推导配套 MD 路径（同目录同名，扩展名替换为 .md）
 function resolveArticleMarkdownPath(docxPath) {
@@ -245,6 +245,7 @@ export async function runDownloadSciArticle(options = {}) {
         produceId,
     });
     const docxPath = resolveArticleDownloadPath(options.output, articleTitle);
+    await mkdir(dirname(docxPath), { recursive: true });
     await writeFile(docxPath, buffer);
     const mdPath = resolveArticleMarkdownPath(docxPath);
     const mdBuffer = Buffer.from(markdown, "utf8");

package/cli/dist/modules/sci/commands/article-download.js.map CHANGED Viewed

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package/cli/dist/modules/sci/precheck-cache.js CHANGED Viewed

@@ -5,7 +5,7 @@
  * 续跑时，须复用首次预检的 level/content，对齐官网 PracticalPrecheck.onOk
  * （选是/否后直接生成提纲，不二次预检）。
  *
- * 与 article-cache 同目录 helixlife-sci-cache/，前缀 precheck-。
+ * 与 article-cache 同目录（helixlife 状态目录 sci/），前缀 precheck-。
  */
 import { randomBytes } from "node:crypto";
 import { chmod, mkdir, readFile, rename, rm, writeFile, } from "node:fs/promises";

package/cli/dist/modules/shared/result-wrapper.d.ts CHANGED Viewed

@@ -13,7 +13,7 @@
  *
  * 包装后的 JSON 结构：
  * {
- *   "_meta": { "step": "...", "subType": "...", "timestamp": "..." },
+ *   "_meta": { "step": "...", "subType": "...", "timestamp": "...", "cliVersion": "..." },
  *   "_handoff": { "orderId": "...", "workflowRunId": "...", "cacheReady": true },  // 可选，仅供 Agent 内存串联
  *   "data": { ...业务结果字段（已剔除禁止对外的内部 ID） }
  * }
@@ -25,13 +25,15 @@ export interface WorkbenchResultMeta {
     step: string;
     subType?: string;
     timestamp: string;
+    /** 当前 CLI 版本，供 Skill 校验 minCliVersion */
+    cliVersion: string;
 }
 export interface WorkbenchResultHandoff {
     orderId?: string;
     /** CLI 本地流程缓存键，不对应后端订单 */
     sessionId?: string;
     workflowRunId?: string;
-    /** 步骤② 全文是否已成功写入系统临时目录缓存（供 Agent 步骤③ 前自检） */
+    /** 步骤② 全文是否已成功写入 CLI 状态目录缓存（供 Agent 步骤③ 前自检） */
     cacheReady?: boolean;
     /** 基金 Step1：blank（无假说）| existing（已有假说） */
     hasHypothesis?: string;

package/cli/dist/modules/shared/result-wrapper.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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