@tryaura/aura-cli 0.2.0 → 0.2.1

package/dist/bin/aura.js

@@ -1,6 +1,6 @@
 #!/usr/bin/env node
-import { n as OFFICIAL_REGISTRY_OPTIONS, t as OFFICIAL_PLUGINS } from "../plugins-SZegBVXF.js";
-import { t as runCli } from "../run.boundary-BtMqQAEQ.js";
+import { n as OFFICIAL_REGISTRY_OPTIONS, t as OFFICIAL_PLUGINS } from "../plugins-Dbasvr1u.js";
+import { t as runCli } from "../run.boundary-CF5kZTH3.js";
 //#endregion
 //#region src/bin.ts
 await runCli({
@@ -9,7 +9,7 @@ await runCli({
 		description: "Agent Unification & Repair Assistant",
 		displayName: "Aura",
 		docsUrl: "https://tryaura.sh/docs/introduction",
-		version: "0.2.0"
+		version: "0.2.1"
 	},
 	plugins: OFFICIAL_PLUGINS,
 	registry: OFFICIAL_REGISTRY_OPTIONS

package/dist/index.js

@@ -1,4 +1,4 @@
-import { i as vetHttpUrl, n as clampHttpTimeout, r as failureReason, t as runCli } from "./run.boundary-BtMqQAEQ.js";
+import { i as vetHttpUrl, n as clampHttpTimeout, r as failureReason, t as runCli } from "./run.boundary-CF5kZTH3.js";
 //#region ../core/src/http-post.boundary.ts
 /**
 * Creates a bounded, TLS-only JSON POST that never rejects.

package/dist/plugins/index.js

@@ -1,2 +1,2 @@
-import { a as codexPlugin, i as claudeCodePlugin, n as OFFICIAL_REGISTRY_OPTIONS, o as cursorPlugin, r as checksCorePlugin, s as officialContentPlugin, t as OFFICIAL_PLUGINS } from "../plugins-SZegBVXF.js";
+import { a as codexPlugin, i as claudeCodePlugin, n as OFFICIAL_REGISTRY_OPTIONS, o as cursorPlugin, r as checksCorePlugin, s as officialContentPlugin, t as OFFICIAL_PLUGINS } from "../plugins-Dbasvr1u.js";
 export { OFFICIAL_PLUGINS, OFFICIAL_REGISTRY_OPTIONS, checksCorePlugin, claudeCodePlugin, codexPlugin, cursorPlugin, officialContentPlugin };

package/dist/{plugins-SZegBVXF.js → plugins-Dbasvr1u.js}

@@ -1,4 +1,4 @@
-import { G as src_default$4, I as createAuraManifestWriteOperation, K as pluralize, S as readManagedBlock, W as SHARED_INSTRUCTIONS_TEMPLATE, _ as planSharedSkillTreeUpdate, b as reconcileManagedSnippet, c as planManifestMcpConvergence, f as isAuraOwnedSkillTarget, g as managedContentRevisionStatus, h as skillDeploymentStatus, i as planMcpSecretRemediation, l as planMcpServerRemoval, m as sharedSkillsRoot, n as canPlanMcpSecretRemediation, o as mcpConvergenceBlockers, p as planSkillDeployment, q as displayPath, t as planSharedInstructionLink, v as reconcileParsedManagedBlock, y as diffManagedSnippet } from "./shared-link-plan-DVgOyqP9.js";
+import { G as src_default$4, I as createAuraManifestWriteOperation, K as pluralize, S as readManagedBlock, W as SHARED_INSTRUCTIONS_TEMPLATE, _ as planSharedSkillTreeUpdate, b as reconcileManagedSnippet, c as planManifestMcpConvergence, f as isAuraOwnedSkillTarget, g as managedContentRevisionStatus, h as skillDeploymentStatus, i as planMcpSecretRemediation, l as planMcpServerRemoval, m as sharedSkillsRoot, n as canPlanMcpSecretRemediation, o as mcpConvergenceBlockers, p as planSkillDeployment, q as displayPath, t as planSharedInstructionLink, v as reconcileParsedManagedBlock, y as diffManagedSnippet } from "./shared-link-plan-D8fxdFYv.js";
 import { EMPTY_COLLECTION, McpWriteError, SHARED_INSTRUCTIONS_TEMPLATE_TOKEN, TIMEOUT_EXIT_CODE, collectJsonMcpServers, collectMcpServers, configStringArray, configStringRecord, defineAdapter, defineCheck, definePlugin, detectExecutable, detectLineEnding, inspectJsonMcpSecrets, isConfigRecord, isFileReference, jsonMcpEntry, jsonMcpSecretTransform, maskMarkdownCode, mcpCommandEntry, mcpEnvironmentVariableNames, mcpWriteResult, normalizeMcpServerDefinition, parseAtImports, parseConfigObject, parseInstalledSkills, parseJsonMcpConfig, redactMcpArguments, referenceTargetPath, sanitizeMcpUrl, skillDirectorySpecs, splitSourceLines, stdioTransport, writeJsonMcpServers } from "@tryaura/aura-sdk";
 import { dirname, extname, isAbsolute, join, resolve, sep } from "node:path";
 import { parse, stringify } from "smol-toml";
@@ -1194,12 +1194,10 @@ function validateToml(content, message) {
 //#endregion
 //#region ../../plugins/adapter-codex/src/project-directories.ts
 /**
-* Every directory of the current project Codex consults, from `cwd` outward to the repository root.
+* Every directory Codex searches for project instructions, from `cwd` to the repository root.
 *
-* Two features need exactly this list. Codex keys `[projects."..."]` by the directory it was
-* launched in, which is frequently a subdirectory of the repository rather than its root, and it
-* reads one `AGENTS.md` per directory from the root down to `cwd`. Both are the same walk read in
-* opposite directions, so they share it rather than each keeping a copy.
+* Codex reads one `AGENTS.md` per directory from the root down to `cwd`. Project trust deliberately
+* does not share this walk: Codex checks only the exact cwd and the primary Git checkout for trust.
 *
 * Without a repository root there is nothing to walk to: every ancestor of the working directory is
 * a different project as far as Codex is concerned, so only `cwd` is considered. The same answer
@@ -1351,11 +1349,10 @@ function remainingBytes(selected, files, remaining) {
 /**
 * Reads the current project's trust marker from Codex's shared configuration.
 *
-* Codex keys `[projects."..."]` by the directory it was launched in, which is frequently a
-* subdirectory of the repository rather than its root. Looking only at the root would report a
-* project as untrusted whenever the developer started Codex from somewhere inside it, so every
-* directory from `cwd` up to and including the repository root is considered and the narrowest
-* recorded answer wins.
+* Codex first checks the exact directory it was launched in, then the primary Git checkout. The
+* second identity matters for linked worktrees: Codex resolves their `.git` pointer back to the
+* main checkout, so trusting that checkout covers every associated worktree unless an exact cwd
+* entry overrides it.
 */
 function parseProjectTrust(file, lookup) {
 	const root = parseConfigObject(file.content, parse);
@@ -1363,7 +1360,7 @@ function parseProjectTrust(file, lookup) {
 	const projects = root["projects"];
 	if (!isConfigRecord(projects)) return "unknown";
 	const entries = new Map(Object.entries(projects).map(([key, value]) => [normalize(key), value]));
-	for (const directory of projectDirectories(lookup)) {
+	for (const directory of trustDirectories(lookup)) {
 		const project = entries.get(directory);
 		if (!isConfigRecord(project)) continue;
 		const trust = project["trust_level"];
@@ -1371,6 +1368,12 @@ function parseProjectTrust(file, lookup) {
 	}
 	return "unknown";
 }
+function trustDirectories(lookup) {
+	const cwd = normalize(lookup.cwd);
+	if (lookup.gitMainWorktreeRoot === void 0) return [cwd];
+	const mainWorktreeRoot = normalize(lookup.gitMainWorktreeRoot);
+	return cwd === mainWorktreeRoot ? [cwd] : [cwd, mainWorktreeRoot];
+}
 /** Collapses separators and trailing slashes so a config key and a scanned path compare equal. */
 function normalize(directory) {
 	return resolve(directory);
@@ -1401,7 +1404,7 @@ const codexAdapter = defineAdapter({
 	mcpWrite: writeMcpServers$1,
 	mcpSecrets: transformMcpSecrets$1,
 	parse: (input) => {
-		const { cwd, files, homeDir, projectRoot } = input;
+		const { cwd, files, gitMainWorktreeRoot, homeDir } = input;
 		const mcp = files.get(CODEX_SOURCE_IDS.mcp);
 		const mcpConfig = mcp === void 0 ? EMPTY_MCP : parseMcpServers$1(mcp);
 		const instructions = selectInstructionFiles(files, {
@@ -1414,7 +1417,7 @@ const codexAdapter = defineAdapter({
 			mcpSecretSightings: mcpConfig.secretSightings ?? [],
 			metadata: { [CODEX_PROJECT_TRUST_KEY]: mcp === void 0 ? "unknown" : parseProjectTrust(mcp, {
 				cwd,
-				projectRoot
+				gitMainWorktreeRoot
 			}) },
 			problems: [...shadowedEntryProblems(instructions.shadowed), ...unusableConfig(mcp, mcpConfig.malformed)],
 			skills: parseInstalledSkills(CODEX_ADAPTER_ID, input, SKILL_DIRECTORIES),
@@ -2162,7 +2165,7 @@ const env004 = defineCheck({
 	detect: (model) => detectConflicts(model),
 	explain: `Claude Code can appear unable to work when its effective default permission mode is plan or dontAsk. Codex skips project-scoped configuration when a project is untrusted, so Aura also reports projects that are not explicitly trusted.
 
-Claude Code: edit the settings file named by the finding and choose default or acceptEdits as appropriate. Codex: edit ~/.codex/config.toml and add a \`[projects."<project-root>"]\` section with \`trust_level = "trusted"\` after reviewing the repository.`,
+Claude Code: edit the settings file named by the finding and choose default or acceptEdits as appropriate. Codex: after reviewing the repository, edit ~/.codex/config.toml and trust the exact working directory or the primary Git checkout. Codex resolves linked worktrees back to that primary checkout.`,
 	fix: (finding, model) => guidedFix$2(finding, model),
 	fixability: "guided",
 	id: "ENV-004",
@@ -2198,7 +2201,7 @@ function codexFindings(app) {
 	if (trust === "trusted" || trust === "unreadable") return [];
 	const path = sourcePath$2(app, CODEX_SOURCE_IDS.mcp);
 	return [{
-		details: trust === "untrusted" ? "Codex explicitly marks this project untrusted and skips its project-scoped configuration." : "Codex has no trusted entry for this project or any directory inside it, so project-scoped configuration may be unavailable until trust is confirmed.",
+		details: trust === "untrusted" ? "Codex explicitly marks this project untrusted and skips its project-scoped configuration." : "Codex has no trusted entry for this working directory or its primary Git checkout, so project-scoped configuration may be unavailable until trust is confirmed.",
 		id: `codex-project-trust:${trust}`,
 		...path === void 0 ? {} : { locations: [{ path }] },
 		message: trust === "untrusted" ? "Codex marks this project as untrusted." : "Codex does not mark this project as trusted.",
@@ -2223,11 +2226,14 @@ function guidedFix$2(finding, model) {
 			summary: "Change Claude Code's restrictive default permission mode."
 		};
 	}
-	if (appId === "codex" && model.projectRoot !== void 0) return {
-		manualSteps: [`After reviewing the repository, add [projects.${JSON.stringify(model.projectRoot)}] with trust_level = "trusted" in ~/.codex/config.toml.`, "Restart Codex in the project and run `aura check` again."],
-		operations: [],
-		summary: "Trust the current project in Codex."
-	};
+	if (appId === "codex" && model.projectRoot !== void 0) {
+		const trustRoot = model.gitMainWorktreeRoot ?? model.cwd;
+		return {
+			manualSteps: [`After reviewing the repository, add [projects.${JSON.stringify(trustRoot)}] with trust_level = "trusted" in ~/.codex/config.toml.`, "Restart Codex in the project and run `aura check` again."],
+			operations: [],
+			summary: "Trust the current project in Codex."
+		};
+	}
 }
 //#endregion
 //#region ../../plugins/checks-core/src/hashing.ts
@@ -2756,7 +2762,7 @@ const legacyInstructionsCheck = defineCheck({
 	detect: (model) => legacyDocuments(model.instructionFiles).map((legacy) => toFinding(legacy, model)),
 	explain: `Legacy instruction files are easy to forget after changing agent applications or configuration formats. They may still be loaded unexpectedly, or hold useful guidance that newer application files never received.
 
-Re-run the check with \`--fix --interactive\` to review the suggested migration steps, then use the \`setup\` command to consolidate selected content. Aura archives originals through its reversible backup history instead of deleting them silently.`,
+Re-run the check with \`--fix\` to review the suggested migration steps, then use the \`setup\` command to consolidate selected content. Aura archives originals through its reversible backup history instead of deleting them silently.`,
 	fix: guidedFix$1,
 	fixability: "guided",
 	id: "INS-004",
@@ -3466,7 +3472,7 @@ const instructionLinkIntegrityCheck = defineCheck({
 	detect: detectLinkProblems,
 	explain: `Instruction imports must point to files the application can load without cycles or excessive nesting. Broken or unsupported chains silently discard guidance and can leave an agent running with only part of the intended instructions.
 
-Re-run the check with \`--fix --interactive\` to review the affected source and target paths. Create or correct missing targets, remove one edge from cycles, and flatten chains that exceed the named application's supported depth.`,
+Re-run the check with \`--fix\` to review the affected source and target paths. Create or correct missing targets, remove one edge from cycles, and flatten chains that exceed the named application's supported depth.`,
 	fix: guidedFix,
 	fixability: "guided",
 	id: "INS-006",
@@ -4457,7 +4463,7 @@ const managedBlockHashCheck = defineCheck({
 	detect: detectManagedBlockDrift,
 	explain: `Aura hashes each managed snippet so hand edits cannot be overwritten silently. A mismatch means the installed text no longer matches the registered version, so a later setup run must not guess which side should win.
 
-Re-run the check with \`--fix --interactive\` and choose Keep yours to adopt the edit, Restore to return to registered content, or Merge to review both versions and reconcile them manually. Every executable choice is previewed and backed up before Aura writes.`,
+Re-run the check with \`--fix\` and choose Keep yours to adopt the edit, Restore to return to registered content, or Merge to review both versions and reconcile them manually. Every executable choice is previewed and backed up before Aura writes.`,
 	fix: () => void 0,
 	fixability: "guided",
 	guidedFixes: guidedFixes$2,
@@ -4479,7 +4485,7 @@ function findingsForDocument(document, model) {
 		const manifestHash = manifestHashes.get(snippet.id);
 		return !snippet.hashMatches || manifestHash !== void 0 && manifestHash !== snippet.computedHash;
 	}).map((snippet) => ({
-		details: "Run `aura check --fix --interactive` and choose Keep yours, Restore, or Merge before running setup again.",
+		details: "Run `aura check --fix` and choose Keep yours, Restore, or Merge before running setup again.",
 		id: `${document.sourceId}:${snippet.id}`,
 		locations: [{
 			line: snippet.startLine,
@@ -4495,7 +4501,7 @@ function findingsForDocument(document, model) {
 }
 function unterminatedFenceFinding(document, line, model) {
 	return {
-		details: "Close the Markdown fence, then run `aura check --fix --interactive` again. Aura will not reconcile this document while its markers are hidden.",
+		details: "Close the Markdown fence, then run `aura check --fix` again. Aura will not reconcile this document while its markers are hidden.",
 		id: `${document.sourceId}:unterminated-fence`,
 		locations: [{
 			...line === void 0 ? {} : { line },
@@ -4697,7 +4703,7 @@ function resolveDriftFirst(contentId) {
 		id: "resolve-drift",
 		label: "Resolve local edits first",
 		plan: {
-			manualSteps: [`Run \`aura check --only MGD-001 --fix --interactive\` and resolve edits to ${contentId}, then review this update again.`],
+			manualSteps: [`Run \`aura check --only MGD-001 --fix\` and resolve edits to ${contentId}, then review this update again.`],
 			operations: [],
 			summary: `Resolve local edits to ${contentId} before updating it.`
 		}
@@ -4717,7 +4723,7 @@ function resolveSkillDriftFirst(contentId) {
 const managedContentUpdateCheck = defineCheck({
 	defaultSeverity: "info",
 	detect: detectManagedContentUpdates,
-	explain: "Aura records the exact version and content hash of each managed snippet and skill. When an installed plugin offers a different revision, Aura reports it and waits for a reviewed change instead of silently replacing managed content. A revision that is not newer — a rollback, or one this build cannot order — is reported too, because Aura keeps the recorded revision either way and an unreported hold would look like nothing to do. Pinned selections remain quiet until they are unpinned.\n\nRun `aura check --fix --interactive` to review bundled revisions and vanished snippets. Locally edited content must be resolved first; directory-sourced skill updates stay in `aura setup`, where network and credential approval are explicit.",
+	explain: "Aura records the exact version and content hash of each managed snippet and skill. When an installed plugin offers a different revision, Aura reports it and waits for a reviewed change instead of silently replacing managed content. A revision that is not newer — a rollback, or one this build cannot order — is reported too, because Aura keeps the recorded revision either way and an unreported hold would look like nothing to do. Pinned selections remain quiet until they are unpinned.\n\nRun `aura check --fix` to review bundled revisions and vanished snippets. Locally edited content must be resolved first; directory-sourced skill updates stay in `aura setup`, where network and credential approval are explicit.",
 	fix: () => void 0,
 	fixability: "guided",
 	guidedFixes: managedContentUpdateChoices,
@@ -5179,7 +5185,7 @@ const mcp003 = defineCheck({
 	detect: detectDeadServers,
 	explain: `Aura checks stdio commands with filesystem-only PATH resolution, and starts no MCP server of its own. Package launchers such as npx, uvx, and bunx are checked, but Aura does not guess whether the requested package is installed or cached.
 
-Remote URLs are silent and generate no network traffic unless \`check --online\` is supplied. Online probes use short, bounded requests without configured authentication headers, and they skip an endpoint whose credentials Aura stripped, because the remaining URL no longer addresses the configured server. A redirect to a private address is reported rather than followed. A timeout or a server-side fault is a warning, not an error: it may not repeat. Re-run with \`--fix --interactive\` to choose whether to repair or remove a server that definitely failed its probe. Cursor separately requires its MCP servers to be approved and enabled in its own settings, which no file records; Aura reads those states by running \`cursor-agent mcp list\` when that CLI is installed and identifies itself. The command is Cursor's, and it connects to servers to answer, so Aura runs it from your home directory: only your own global configuration takes part, never a \`.cursor/mcp.json\` committed to the repository you are in. Aura never approves, enables, or retries a server itself, and every state it reports this way is a warning. Aura also reports an informational reminder when a desired MCP transport references an unset environment variable. It retains only the variable name and whether it is set; credential values never enter the workspace model or report.`,
+Remote URLs are silent and generate no network traffic unless \`check --online\` is supplied. Online probes use short, bounded requests without configured authentication headers, and they skip an endpoint whose credentials Aura stripped, because the remaining URL no longer addresses the configured server. A redirect to a private address is reported rather than followed. A timeout or a server-side fault is a warning, not an error: it may not repeat. Re-run with \`--fix\` to choose whether to repair or remove a server that definitely failed its probe. Cursor separately requires its MCP servers to be approved and enabled in its own settings, which no file records; Aura reads those states by running \`cursor-agent mcp list\` when that CLI is installed and identifies itself. The command is Cursor's, and it connects to servers to answer, so Aura runs it from your home directory: only your own global configuration takes part, never a \`.cursor/mcp.json\` committed to the repository you are in. Aura never approves, enables, or retries a server itself, and every state it reports this way is a warning. Aura also reports an informational reminder when a desired MCP transport references an unset environment variable. It retains only the variable name and whether it is set; credential values never enter the workspace model or report.`,
 	fix: () => void 0,
 	fixability: "guided",
 	guidedFixes: guidedFixes$1,
@@ -5317,7 +5323,7 @@ const mcp004 = defineCheck({
 	detect: detectInlineSecrets,
 	explain: `Inline credentials in MCP configuration can leak through source control, logs, diagnostics, and copied configuration. Aura identifies credential-bearing fields without retaining their values, prefixes, or lengths.
 
-Re-run with \`--fix --interactive\` to replace every behavior-preserving sighting in the same source file with an environment reference. Copy the current values directly from the named file before applying the rewrite; Aura never displays or stores those values outside the protected undo payload, which stays owner-only under \`~/agents/.backups\` until twenty later fixes have pushed it out of the journal. Then rotate each credential at its issuer: moving a value behind an environment reference stops it leaking again, not from wherever it has already reached.`,
+Re-run with \`--fix\` to replace every behavior-preserving sighting in the same source file with an environment reference. Copy the current values directly from the named file before applying the rewrite; Aura never displays or stores those values outside the protected undo payload, which stays owner-only under \`~/agents/.backups\` until twenty later fixes have pushed it out of the journal. Then rotate each credential at its issuer: moving a value behind an environment reference stops it leaking again, not from wherever it has already reached.`,
 	findingGroup: {
 		description: "Replace inline credentials with environment-variable references.",
 		id: "checks-core/mcp-credentials",
@@ -5557,7 +5563,7 @@ const mcp005 = defineCheck({
 	detect: detectScopePlacement,
 	explain: `The Aura manifest distinguishes personal MCP servers from team servers. Personal servers belong in global configuration; putting one in repository configuration can publish it to teammates through source control. Team servers belong in project configuration; keeping one only in personal configuration means teammates do not receive it and their setup drifts. Placement is judged by the file an entry is written in, not by the scope label alone, because an application can keep both kinds in one document.
 
-Re-run with \`--fix --interactive\` to move an Aura-owned entry through the same manifest convergence and undo machinery as other MCP fixes. Aura never removes a name outside its ownership ledger automatically.`,
+Re-run with \`--fix\` to move an Aura-owned entry through the same manifest convergence and undo machinery as other MCP fixes. Aura never removes a name outside its ownership ledger automatically.`,
 	fix: placementFix,
 	fixability: "guided",
 	id: MCP_005_ID,