skills-doctor 0.5.0 → 0.5.2

package/CHANGELOG.md

@@ -6,6 +6,22 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 
 ## [Unreleased]
 
+## [0.5.2] - 2026-06-20
+
+### Added
+
+- Let users choose which unused cleanup candidates to include in cleanup handoff prompts.
+
+### Changed
+
+- Include all unused cleanup candidates in reports and handoff selection instead of capping the detected list.
+
+## [0.5.1] - 2026-06-20
+
+### Changed
+
+- Store default repair and cleanup handoff reports under the OS temp directory instead of creating `.skills-doctor/reports` in the scanned project.
+
 ## [0.5.0] - 2026-06-20
 
 ### Added

package/README.md

@@ -104,7 +104,8 @@ available, reads local Codex usage traces from known `~/.codex` paths. It can:
 3. Let you choose a repair subset: errors, errors plus warnings, all findings,
    or selected skills.
 4. Detect local `claude` and `codex` executables.
-5. Write a full report under `.skills-doctor/reports/<timestamp>/`.
+5. Write a full report under the OS temp directory, for example
+   `/tmp/skills-doctor-<uid>/reports/<timestamp>/` on Linux.
 6. Generate a compact `handoff-prompt.md` tailored to the selected findings or
    `cleanup-prompt.md` tailored to usage cleanup.
 7. Preview the launch command.

package/dist/cli/commands/scan.js

@@ -300,7 +300,7 @@ const reviewScan = async (report, input) => {
             ...(report.usage !== undefined && report.usage.topRecommendations.length > 0
                 ? [
                     {
-                        name: "Disable unused skills to reduce context pressure",
+                        name: "Choose unused skills to disable",
                         value: "cleanup",
                     },
                     { name: "View usage ranking", value: "usage-ranking" },
@@ -350,8 +350,14 @@ const reviewScan = async (report, input) => {
 };
 const runCleanupAgentFlow = async (report, input) => {
     try {
+        const selectedRecommendations = await selectCleanupRecommendations(report, input);
+        if (selectedRecommendations.length === 0) {
+            input.write("Cleanup handoff cancelled.\n");
+            return undefined;
+        }
         const handoff = await prepareCleanupHandoff({
             report,
+            recommendations: selectedRecommendations,
             outputRoot: input.cleanupReportOutputRoot,
             timestamp: input.cleanupReportTimestamp,
         });
@@ -427,6 +433,22 @@ const runCleanupAgentFlow = async (report, input) => {
         throw error;
     }
 };
+const selectCleanupRecommendations = async (report, input) => {
+    const usage = report.usage;
+    if (usage === undefined)
+        throw new CliInputError("Usage analysis is required before cleanup.");
+    const candidates = usage.recommendations.filter((recommendation) => recommendation.action === "disable-candidate");
+    if (candidates.length === 0)
+        return [];
+    const defaultPaths = new Set(usage.topRecommendations.map((recommendation) => recommendation.skillPath));
+    const selectedPaths = new Set(await input.prompts.checkbox("Select unused skills to disable", candidates.map((recommendation) => ({
+        name: recommendation.skillName,
+        value: recommendation.skillPath,
+        description: compactSkillPath(recommendation.skillPath),
+        checked: defaultPaths.has(recommendation.skillPath),
+    }))));
+    return candidates.filter((recommendation) => selectedPaths.has(recommendation.skillPath));
+};
 const runRepairAgentFlow = async (report, input) => {
     try {
         const handoff = await prepareRepairHandoff({

package/dist/cli/utils/cleanup-handoff-to-agent.d.ts

@@ -1,3 +1,4 @@
+import type { SkillCleanupRecommendation } from "../../domain/analyze-skill-usage.js";
 import type { ScanReport } from "../../domain/build-report.js";
 import { writeCleanupDirectory } from "../../domain/write-cleanup-directory.js";
 export type PreparedCleanupHandoff = {
@@ -10,6 +11,7 @@ export type PreparedCleanupHandoff = {
 };
 export type PrepareCleanupHandoffInput = {
     readonly report: ScanReport;
+    readonly recommendations?: readonly SkillCleanupRecommendation[] | undefined;
     readonly outputRoot?: string | undefined;
     readonly timestamp?: string | undefined;
     readonly writeDirectory?: typeof writeCleanupDirectory | undefined;

package/dist/cli/utils/cleanup-handoff-to-agent.d.ts.map

@@ -1 +1 @@
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package/dist/cli/utils/cleanup-handoff-to-agent.js

@@ -10,6 +10,12 @@ export const prepareCleanupHandoff = async (input) => {
     if (input.report.usage.topRecommendations.length === 0) {
         throw new CliInputError("No cleanup recommendations are available.");
     }
+    if (input.recommendations !== undefined && input.recommendations.length === 0) {
+        throw new CliInputError("No cleanup recommendations were selected.");
+    }
+    if (input.recommendations?.some((recommendation) => recommendation.action !== "disable-candidate")) {
+        throw new CliInputError("Cleanup handoff can only disable selected unused skills.");
+    }
     const reportResult = await tryWriteCleanupDirectory({
         report: input.report,
         outputRoot: input.outputRoot,
@@ -18,6 +24,7 @@ export const prepareCleanupHandoff = async (input) => {
     });
     const prompt = buildCleanupHandoffPrompt({
         report: input.report,
+        recommendations: input.recommendations,
         reportDirectory: reportResult.result?.directory,
     });
     let promptPath;

package/dist/cli/utils/prompts.d.ts

@@ -3,6 +3,7 @@ export type Choice<Value extends string> = {
     readonly name: string;
     readonly value: Value;
     readonly description?: string;
+    readonly checked?: boolean;
 };
 export type PromptAdapter = {
     readonly checkbox: <Value extends string>(message: string, choices: readonly Choice<Value>[]) => Promise<Value[]>;

package/dist/cli/utils/prompts.d.ts.map

@@ -1 +1 @@
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package/dist/domain/build-cleanup-handoff-prompt.d.ts

@@ -1,6 +1,8 @@
+import type { SkillCleanupRecommendation } from "./analyze-skill-usage.js";
 import type { ScanReport } from "./build-report.js";
 export type BuildCleanupHandoffPromptInput = {
     readonly report: ScanReport;
+    readonly recommendations?: readonly SkillCleanupRecommendation[] | undefined;
     readonly reportDirectory?: string | undefined;
 };
 export declare const buildCleanupHandoffPrompt: (input: BuildCleanupHandoffPromptInput) => string;

package/dist/domain/build-cleanup-handoff-prompt.d.ts.map

@@ -1 +1 @@
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package/dist/domain/build-cleanup-handoff-prompt.js

@@ -1,5 +1,6 @@
 export const buildCleanupHandoffPrompt = (input) => {
     const usage = requireUsage(input.report);
+    const recommendations = input.recommendations ?? usage.topRecommendations;
     const lines = [
         "Clean up Agent Skills context pressure using the Skills Doctor usage report.",
         "",
@@ -15,12 +16,12 @@ export const buildCleanupHandoffPrompt = (input) => {
     else {
         lines.push("Usage report directory: unavailable; use the inline summary below.");
     }
-    lines.push("", "Cleanup rules:", "- Inspect the usage report first.", "- Preserve frequently used and recently used skills.", "- Preserve project-local skills unless there is strong evidence and clear user intent.", "- Do not delete skills.", "- Only disable skills with a `disable-candidate` recommendation.", "- Do not modify skills recommended as keep, review, shorten-description, or merge-candidate.", "- Do not move skill directories.", "- For unused global/plugin skills, disable them the same way Codex `/skills` does: add or update `[[skills.config]]` entries in `~/.codex/config.toml` with the skill `path` and `enabled = false`.", "- Re-enable skills by using Codex `/skills` or removing the matching disabled config entry.", "- Restart Codex or start a fresh session after config changes so the disabled skill list is reloaded.", "- Do not delete skills solely because usage is unknown.", "- Do not expose raw Codex logs or transcript text.", "- Verify by rerunning `npx skills-doctor@latest` after changes.", "", "Unused skills to disable:");
-    for (const recommendation of usage.topRecommendations.slice(0, 20)) {
+    lines.push("", "Cleanup rules:", "- Inspect the usage report first.", "- Preserve frequently used and recently used skills.", "- Preserve project-local skills unless there is strong evidence and clear user intent.", "- Do not delete skills.", "- Only disable skills with a `disable-candidate` recommendation.", "- Disable only the selected skills listed below; leave other cleanup candidates unchanged.", "- Do not modify skills recommended as keep, review, shorten-description, or merge-candidate.", "- Do not move skill directories.", "- For unused global/plugin skills, disable them the same way Codex `/skills` does: add or update `[[skills.config]]` entries in `~/.codex/config.toml` with the skill `path` and `enabled = false`.", "- Re-enable skills by using Codex `/skills` or removing the matching disabled config entry.", "- Restart Codex or start a fresh session after config changes so the disabled skill list is reloaded.", "- Do not delete skills solely because usage is unknown.", "- Do not expose raw Codex logs or transcript text.", "- Verify by rerunning `npx skills-doctor@latest` after changes.", "", "Selected unused skills to disable:");
+    for (const recommendation of recommendations) {
         lines.push(`- ${recommendation.action} ${recommendation.skillName}`, `  Path: ${recommendation.skillPath}`, `  Reason: ${recommendation.reason}`);
     }
-    if (usage.topRecommendations.length === 0) {
-        lines.push("- No unused disable candidates were produced.");
+    if (recommendations.length === 0) {
+        lines.push("- No unused disable candidates were selected.");
     }
     lines.push("", "Make only reversible Codex skills-config disable changes, then stop and report what changed.");
     return lines.join("\n");

package/dist/domain/build-report.d.ts

@@ -57,7 +57,6 @@ export type BuildScanReportInput = {
 export type BuildScanReportUsageInput = {
     readonly analysis: SkillUsageAnalysis;
     readonly contextPressure: ContextBudgetPressure;
-    readonly topRecommendationLimit?: number | undefined;
 };
 export declare const buildScanReport: (input: BuildScanReportInput) => ScanReport;
 //# sourceMappingURL=build-report.d.ts.map

package/dist/domain/build-report.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"build-report.d.ts","sourceRoot":"","sources":["../../src/domain/build-report.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EACV,0BAA0B,EAC1B,kBAAkB,EAClB,iBAAiB,EAClB,MAAM,0BAA0B,CAAC;AAClC,OAAO,EAAkB,KAAK,YAAY,EAAE,MAAM,sBAAsB,CAAC;AACzE,OAAO,KAAK,EAAE,qBAAqB,EAAE,MAAM,6BAA6B,CAAC;AAEzE,OAAO,KAAK,EAAE,UAAU,EAAE,OAAO,EAAE,UAAU,EAAE,SAAS,EAAE,MAAM,YAAY,CAAC;AAE7E,MAAM,MAAM,YAAY,GAAG;IACzB,QAAQ,CAAC,SAAS,EAAE,MAAM,CAAC;IAC3B,QAAQ,CAAC,IAAI,EAAE,MAAM,CAAC;IACtB,QAAQ,CAAC,aAAa,EAAE,MAAM,CAAC;IAC/B,QAAQ,CAAC,SAAS,EAAE,MAAM,CAAC;IAC3B,QAAQ,CAAC,YAAY,EAAE,MAAM,CAAC;IAC9B,QAAQ,CAAC,UAAU,EAAE,MAAM,CAAC;IAC5B,QAAQ,CAAC,YAAY,EAAE,MAAM,CAAC;IAC9B,QAAQ,CAAC,WAAW,EAAE,MAAM,CAAC;CAC9B,CAAC;AAEF,MAAM,MAAM,UAAU,GAAG;IACvB,QAAQ,CAAC,aAAa,EAAE,CAAC,CAAC;IAC1B,QAAQ,CAAC,EAAE,EAAE,OAAO,CAAC;IACrB,QAAQ,CAAC,OAAO,EAAE,MAAM,CAAC;IACzB,QAAQ,CAAC,SAAS,EAAE,MAAM,CAAC;IAC3B,QAAQ,CAAC,mBAAmB,EAAE,MAAM,CAAC;IACrC,QAAQ,CAAC,YAAY,EAAE,SAAS,SAAS,EAAE,CAAC;IAC5C,QAAQ,CAAC,WAAW,EAAE,SAAS,UAAU,EAAE,CAAC;IAC5C,QAAQ,CAAC,UAAU,EAAE,MAAM,CAAC;IAC5B,QAAQ,CAAC,YAAY,EAAE,MAAM,CAAC;IAC9B,QAAQ,CAAC,UAAU,EAAE,MAAM,CAAC;IAC5B,QAAQ,CAAC,YAAY,EAAE,MAAM,CAAC;IAC9B,QAAQ,CAAC,WAAW,EAAE,MAAM,CAAC;IAC7B,QAAQ,CAAC,KAAK,EAAE,YAAY,CAAC;IAC7B,QAAQ,CAAC,MAAM,EAAE,SAAS,YAAY,EAAE,CAAC;IACzC,QAAQ,CAAC,QAAQ,EAAE,SAAS,OAAO,EAAE,CAAC;IACtC,QAAQ,CAAC,KAAK,CAAC,EAAE,eAAe,GAAG,SAAS,CAAC;IAC7C,QAAQ,CAAC,gBAAgB,EAAE,OAAO,CAAC;CACpC,CAAC;AAEF,MAAM,MAAM,eAAe,GAAG;IAC5B,QAAQ,CAAC,WAAW,EAAE,SAAS,MAAM,EAAE,CAAC;IACxC,QAAQ,CAAC,mBAAmB,EAAE,MAAM,CAAC;IACrC,QAAQ,CAAC,WAAW,EAAE,SAAS,UAAU,EAAE,CAAC;IAC5C,QAAQ,CAAC,eAAe,EAAE,qBAAqB,CAAC;IAChD,QAAQ,CAAC,mBAAmB,EAAE,MAAM,CAAC;IACrC,QAAQ,CAAC,cAAc,EAAE,MAAM,CAAC;IAChC,QAAQ,CAAC,gBAAgB,EAAE,MAAM,CAAC;IAClC,QAAQ,CAAC,iBAAiB,EAAE,MAAM,CAAC;IACnC,QAAQ,CAAC,mBAAmB,EAAE,MAAM,CAAC;IACrC,QAAQ,CAAC,2BAA2B,EAAE,MAAM,CAAC;IAC7C,QAAQ,CAAC,aAAa,EAAE,SAAS,iBAAiB,EAAE,CAAC;IACrD,QAAQ,CAAC,eAAe,EAAE,SAAS,0BAA0B,EAAE,CAAC;IAChE,QAAQ,CAAC,kBAAkB,EAAE,SAAS,0BAA0B,EAAE,CAAC;CACpE,CAAC;AAEF,MAAM,MAAM,oBAAoB,GAAG;IACjC,QAAQ,CAAC,OAAO,EAAE,MAAM,CAAC;IACzB,QAAQ,CAAC,SAAS,EAAE,MAAM,CAAC;IAC3B,QAAQ,CAAC,mBAAmB,EAAE,MAAM,CAAC;IACrC,QAAQ,CAAC,IAAI,EAAE,UAAU,CAAC;IAC1B,QAAQ,CAAC,KAAK,CAAC,EAAE,yBAAyB,GAAG,SAAS,CAAC;IACvD,QAAQ,CAAC,gBAAgB,CAAC,EAAE,OAAO,CAAC;CACrC,CAAC;AAEF,MAAM,MAAM,yBAAyB,GAAG;IACtC,QAAQ,CAAC,QAAQ,EAAE,kBAAkB,CAAC;IACtC,QAAQ,CAAC,eAAe,EAAE,qBAAqB,CAAC;CACjD,CAAC;AAEF,eAAO,MAAM,eAAe,GAAI,OAAO,oBAAoB,KAAG,UA6C7D,CAAC"}

package/dist/domain/build-report.js

@@ -58,9 +58,7 @@ const buildReportUsage = (input) => ({
     pluginContributedSkillCount: input.analysis.pluginContributedSkillCount,
     skillsByUsage: input.analysis.skillsByUsage,
     recommendations: input.analysis.recommendations,
-    topRecommendations: input.analysis.recommendations
-        .filter((recommendation) => recommendation.action === "disable-candidate")
-        .slice(0, input.topRecommendationLimit ?? 10),
+    topRecommendations: input.analysis.recommendations.filter((recommendation) => recommendation.action === "disable-candidate"),
 });
 const countSeverity = (findings, severity) => findings.filter((finding) => finding.severity === severity).length;
 const countDiagnosticSeverity = (diagnostics, severity) => diagnostics.filter((diagnostic) => diagnostic.severity === severity).length;

package/dist/domain/default-report-output-root.d.ts

@@ -0,0 +1,2 @@
+export declare const defaultReportOutputRoot: () => string;
+//# sourceMappingURL=default-report-output-root.d.ts.map

package/dist/domain/default-report-output-root.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"default-report-output-root.d.ts","sourceRoot":"","sources":["../../src/domain/default-report-output-root.ts"],"names":[],"mappings":"AAGA,eAAO,MAAM,uBAAuB,QAAO,MACgB,CAAC"}

package/dist/domain/default-report-output-root.js

@@ -0,0 +1,19 @@
+import { tmpdir, userInfo } from "node:os";
+import path from "node:path";
+export const defaultReportOutputRoot = () => path.join(tmpdir(), scopedTempDirectoryName(), "reports");
+const scopedTempDirectoryName = () => {
+    const uid = process.getuid?.();
+    if (uid !== undefined) {
+        return `skills-doctor-${uid}`;
+    }
+    try {
+        return `skills-doctor-${safePathSegment(userInfo().username)}`;
+    }
+    catch {
+        return "skills-doctor-user";
+    }
+};
+const safePathSegment = (value) => value
+    .toLowerCase()
+    .replace(/[^a-z0-9._-]+/g, "-")
+    .replace(/^-+|-+$/g, "") || "user";

package/dist/domain/summarize-findings.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"summarize-findings.d.ts","sourceRoot":"","sources":["../../src/domain/summarize-findings.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,UAAU,EAAE,MAAM,mBAAmB,CAAC;AACpD,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,YAAY,CAAC;AAE1C,MAAM,MAAM,gBAAgB,GAAG,OAAO,CAAC,UAAU,CAAC,CAAC;AAEnD,MAAM,MAAM,mBAAmB,GAAG;IAChC,QAAQ,CAAC,MAAM,CAAC,EAAE,gBAAgB,GAAG,SAAS,CAAC;IAC/C,QAAQ,CAAC,QAAQ,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;CACxC,CAAC;AAEF,MAAM,MAAM,cAAc,GAAG;IAC3B,QAAQ,CAAC,UAAU,EAAE,MAAM,CAAC;IAC5B,QAAQ,CAAC,YAAY,EAAE,MAAM,CAAC;IAC9B,QAAQ,CAAC,WAAW,EAAE,MAAM,CAAC;IAC7B,QAAQ,CAAC,SAAS,EAAE,SAAS,YAAY,EAAE,CAAC;IAC5C,QAAQ,CAAC,aAAa,EAAE,SAAS,YAAY,EAAE,CAAC;CACjD,CAAC;AAEF,MAAM,MAAM,YAAY,GAAG;IACzB,QAAQ,CAAC,GAAG,EAAE,MAAM,CAAC;IACrB,QAAQ,CAAC,KAAK,EAAE,MAAM,CAAC;CACxB,CAAC;AAEF,MAAM,MAAM,yBAAyB,GAAG;IACtC,QAAQ,CAAC,YAAY,CAAC,EAAE,OAAO,GAAG,SAAS,CAAC;IAC5C,QAAQ,CAAC,KAAK,CAAC,EAAE,OAAO,GAAG,SAAS,CAAC;CACtC,CAAC;AAEF,eAAO,MAAM,iBAAiB,GAAI,UAAU,SAAS,OAAO,EAAE,KAAG,cAY/D,CAAC;AAEH,eAAO,MAAM,mBAAmB,GAC9B,QAAQ,UAAU,EAClB,UAAS,mBAAwB,KAChC,CAAC,GAAG,CAQN,CAAC;AAEF,eAAO,MAAM,kBAAkB,GAC7B,QAAQ,UAAU,EAClB,UAAS,yBAA8B,KACtC,MAwCF,CAAC"}
+{"version":3,"file":"summarize-findings.d.ts","sourceRoot":"","sources":["../../src/domain/summarize-findings.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,UAAU,EAAE,MAAM,mBAAmB,CAAC;AACpD,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,YAAY,CAAC;AAE1C,MAAM,MAAM,gBAAgB,GAAG,OAAO,CAAC,UAAU,CAAC,CAAC;AAEnD,MAAM,MAAM,mBAAmB,GAAG;IAChC,QAAQ,CAAC,MAAM,CAAC,EAAE,gBAAgB,GAAG,SAAS,CAAC;IAC/C,QAAQ,CAAC,QAAQ,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;CACxC,CAAC;AAEF,MAAM,MAAM,cAAc,GAAG;IAC3B,QAAQ,CAAC,UAAU,EAAE,MAAM,CAAC;IAC5B,QAAQ,CAAC,YAAY,EAAE,MAAM,CAAC;IAC9B,QAAQ,CAAC,WAAW,EAAE,MAAM,CAAC;IAC7B,QAAQ,CAAC,SAAS,EAAE,SAAS,YAAY,EAAE,CAAC;IAC5C,QAAQ,CAAC,aAAa,EAAE,SAAS,YAAY,EAAE,CAAC;CACjD,CAAC;AAEF,MAAM,MAAM,YAAY,GAAG;IACzB,QAAQ,CAAC,GAAG,EAAE,MAAM,CAAC;IACrB,QAAQ,CAAC,KAAK,EAAE,MAAM,CAAC;CACxB,CAAC;AAEF,MAAM,MAAM,yBAAyB,GAAG;IACtC,QAAQ,CAAC,YAAY,CAAC,EAAE,OAAO,GAAG,SAAS,CAAC;IAC5C,QAAQ,CAAC,KAAK,CAAC,EAAE,OAAO,GAAG,SAAS,CAAC;CACtC,CAAC;AAEF,eAAO,MAAM,iBAAiB,GAAI,UAAU,SAAS,OAAO,EAAE,KAAG,cAY/D,CAAC;AAEH,eAAO,MAAM,mBAAmB,GAC9B,QAAQ,UAAU,EAClB,UAAS,mBAAwB,KAChC,CAAC,GAAG,CAQN,CAAC;AAEF,eAAO,MAAM,kBAAkB,GAC7B,QAAQ,UAAU,EAClB,UAAS,yBAA8B,KACtC,MAmCF,CAAC"}

package/dist/domain/summarize-findings.js

@@ -36,11 +36,7 @@ export const renderHumanSummary = (report, options = {}) => {
         }
         const cleanupCandidateCount = countCleanupCandidates(report);
         if (cleanupCandidateCount > 0) {
-            const shownCount = report.usage.topRecommendations.length;
-            const shownSuffix = shownCount < cleanupCandidateCount
-                ? ` (${warning(String(shownCount), shouldColor)} shown in next cleanup batch)`
-                : "";
-            lines.push(`${label("Cleanup candidates", shouldColor)}: ${warning(String(cleanupCandidateCount), shouldColor)} enabled unused skills${shownSuffix}`);
+            lines.push(`${label("Cleanup candidates", shouldColor)}: ${warning(String(cleanupCandidateCount), shouldColor)} enabled unused skills`);
         }
     }
     return `${lines.join("\n")}\n`;

package/dist/domain/write-cleanup-directory.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"write-cleanup-directory.d.ts","sourceRoot":"","sources":["../../src/domain/write-cleanup-directory.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,UAAU,EAAmB,MAAM,mBAAmB,CAAC;AAErE,MAAM,MAAM,qBAAqB,GAAG;IAClC,QAAQ,CAAC,MAAM,EAAE,UAAU,CAAC;IAC5B,QAAQ,CAAC,UAAU,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;IACzC,QAAQ,CAAC,SAAS,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;CACzC,CAAC;AAEF,MAAM,MAAM,sBAAsB,GAAG;IACnC,QAAQ,CAAC,SAAS,EAAE,MAAM,CAAC;IAC3B,QAAQ,CAAC,aAAa,EAAE,MAAM,CAAC;IAC/B,QAAQ,CAAC,iBAAiB,EAAE,MAAM,CAAC;CACpC,CAAC;AAEF,eAAO,MAAM,qBAAqB,GAChC,OAAO,qBAAqB,KAC3B,OAAO,CAAC,sBAAsB,CA+BhC,CAAC"}
+{"version":3,"file":"write-cleanup-directory.d.ts","sourceRoot":"","sources":["../../src/domain/write-cleanup-directory.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,UAAU,EAAmB,MAAM,mBAAmB,CAAC;AAGrE,MAAM,MAAM,qBAAqB,GAAG;IAClC,QAAQ,CAAC,MAAM,EAAE,UAAU,CAAC;IAC5B,QAAQ,CAAC,UAAU,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;IACzC,QAAQ,CAAC,SAAS,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;CACzC,CAAC;AAEF,MAAM,MAAM,sBAAsB,GAAG;IACnC,QAAQ,CAAC,SAAS,EAAE,MAAM,CAAC;IAC3B,QAAQ,CAAC,aAAa,EAAE,MAAM,CAAC;IAC/B,QAAQ,CAAC,iBAAiB,EAAE,MAAM,CAAC;CACpC,CAAC;AAEF,eAAO,MAAM,qBAAqB,GAChC,OAAO,qBAAqB,KAC3B,OAAO,CAAC,sBAAsB,CAgChC,CAAC"}

package/dist/domain/write-cleanup-directory.js

@@ -1,9 +1,11 @@
 import { mkdir, writeFile } from "node:fs/promises";
 import path from "node:path";
+import { defaultReportOutputRoot } from "./default-report-output-root.js";
 export const writeCleanupDirectory = async (input) => {
     const usage = requireUsage(input.report);
-    const directory = path.join(input.outputRoot ?? path.join(input.report.directory, ".skills-doctor", "reports"), sanitizeTimestamp(input.timestamp ?? new Date().toISOString()));
-    await mkdir(directory, { recursive: true });
+    const outputRoot = input.outputRoot ?? defaultReportOutputRoot();
+    const directory = path.join(outputRoot, sanitizeTimestamp(input.timestamp ?? new Date().toISOString()));
+    await mkdir(directory, { recursive: true, mode: 0o700 });
     const usageJsonPath = path.join(directory, "usage.json");
     const usageMarkdownPath = path.join(directory, "usage.md");
     await writeFile(usageJsonPath, `${JSON.stringify({

package/dist/domain/write-findings-directory.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"write-findings-directory.d.ts","sourceRoot":"","sources":["../../src/domain/write-findings-directory.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,UAAU,EAAE,MAAM,mBAAmB,CAAC;AAEpD,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,YAAY,CAAC;AAE1C,MAAM,MAAM,sBAAsB,GAAG;IACnC,QAAQ,CAAC,MAAM,EAAE,UAAU,CAAC;IAC5B,QAAQ,CAAC,QAAQ,CAAC,EAAE,SAAS,OAAO,EAAE,GAAG,SAAS,CAAC;IACnD,QAAQ,CAAC,UAAU,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;IACzC,QAAQ,CAAC,SAAS,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;CACzC,CAAC;AAEF,MAAM,MAAM,uBAAuB,GAAG;IACpC,QAAQ,CAAC,SAAS,EAAE,MAAM,CAAC;IAC3B,QAAQ,CAAC,gBAAgB,EAAE,MAAM,CAAC;IAClC,QAAQ,CAAC,oBAAoB,EAAE,MAAM,CAAC;IACtC,QAAQ,CAAC,gBAAgB,EAAE,SAAS,MAAM,EAAE,CAAC;CAC9C,CAAC;AAEF,eAAO,MAAM,sBAAsB,GACjC,OAAO,sBAAsB,KAC5B,OAAO,CAAC,uBAAuB,CAgDjC,CAAC"}
+{"version":3,"file":"write-findings-directory.d.ts","sourceRoot":"","sources":["../../src/domain/write-findings-directory.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,UAAU,EAAE,MAAM,mBAAmB,CAAC;AAGpD,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,YAAY,CAAC;AAE1C,MAAM,MAAM,sBAAsB,GAAG;IACnC,QAAQ,CAAC,MAAM,EAAE,UAAU,CAAC;IAC5B,QAAQ,CAAC,QAAQ,CAAC,EAAE,SAAS,OAAO,EAAE,GAAG,SAAS,CAAC;IACnD,QAAQ,CAAC,UAAU,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;IACzC,QAAQ,CAAC,SAAS,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;CACzC,CAAC;AAEF,MAAM,MAAM,uBAAuB,GAAG;IACpC,QAAQ,CAAC,SAAS,EAAE,MAAM,CAAC;IAC3B,QAAQ,CAAC,gBAAgB,EAAE,MAAM,CAAC;IAClC,QAAQ,CAAC,oBAAoB,EAAE,MAAM,CAAC;IACtC,QAAQ,CAAC,gBAAgB,EAAE,SAAS,MAAM,EAAE,CAAC;CAC9C,CAAC;AAEF,eAAO,MAAM,sBAAsB,GACjC,OAAO,sBAAsB,KAC5B,OAAO,CAAC,uBAAuB,CAiDjC,CAAC"}

package/dist/domain/write-findings-directory.js

@@ -1,12 +1,14 @@
 import { createHash } from "node:crypto";
 import { mkdir, writeFile } from "node:fs/promises";
 import path from "node:path";
+import { defaultReportOutputRoot } from "./default-report-output-root.js";
 import { groupFindingsByKey } from "./group-findings.js";
 export const writeFindingsDirectory = async (input) => {
     const findings = input.findings ?? input.report.findings;
-    const directory = path.join(input.outputRoot ?? path.join(input.report.directory, ".skills-doctor", "reports"), sanitizeTimestamp(input.timestamp ?? new Date().toISOString()));
+    const outputRoot = input.outputRoot ?? defaultReportOutputRoot();
+    const directory = path.join(outputRoot, sanitizeTimestamp(input.timestamp ?? new Date().toISOString()));
     const skillDirectory = path.join(directory, "skills");
-    await mkdir(skillDirectory, { recursive: true });
+    await mkdir(skillDirectory, { recursive: true, mode: 0o700 });
     const findingsJsonPath = path.join(directory, "findings.json");
     const findingsMarkdownPath = path.join(directory, "findings.md");
     const skillReportPaths = [];

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "skills-doctor",
-  "version": "0.5.0",
+  "version": "0.5.2",
   "description": "Interactive CLI that scans and repairs Agent Skills quality issues.",
   "type": "module",
   "packageManager": "bun@1.3.13",