@grunnverk/kodrdriv 1.3.0

package/dist/arguments.js

@@ -0,0 +1,1307 @@
+import { Command } from 'commander';
+import path from 'path';
+import { z } from 'zod';
+import { PROGRAM_NAME, VERSION, BUILD_HOSTNAME, BUILD_TIMESTAMP, KODRDRIV_DEFAULTS, ALLOWED_COMMANDS, DEFAULT_COMMAND } from './constants.js';
+import { getLogger } from './logging.js';
+import { readStdin, createStorage } from '@grunnverk/shared';
+import { safeJsonParse } from '@grunnverk/git-tools';
+
+z.object({
+    dryRun: z.boolean().optional(),
+    verbose: z.boolean().optional(),
+    debug: z.boolean().optional(),
+    overrides: z.boolean().optional(),
+    checkConfig: z.boolean().optional(),
+    initConfig: z.boolean().optional(),
+    model: z.string().optional(),
+    openaiReasoning: z.enum([
+        'low',
+        'medium',
+        'high'
+    ]).optional(),
+    openaiMaxOutputTokens: z.number().optional(),
+    contextDirectories: z.array(z.string()).optional(),
+    configDir: z.string().optional(),
+    outputDir: z.string().optional(),
+    preferencesDir: z.string().optional(),
+    cached: z.boolean().optional(),
+    add: z.boolean().optional(),
+    sendit: z.boolean().optional(),
+    interactive: z.boolean().optional(),
+    amend: z.boolean().optional(),
+    from: z.string().optional(),
+    to: z.string().optional(),
+    targetVersion: z.string().optional(),
+    skipAlreadyPublished: z.boolean().optional(),
+    forceRepublish: z.boolean().optional(),
+    skipLinkCleanup: z.boolean().optional(),
+    excludedPatterns: z.array(z.string()).optional(),
+    excludedPaths: z.array(z.string()).optional(),
+    exclude: z.array(z.string()).optional(),
+    context: z.string().optional(),
+    contextFiles: z.array(z.string()).optional(),
+    note: z.string().optional(),
+    direction: z.string().optional(),
+    messageLimit: z.number().optional(),
+    skipFileCheck: z.boolean().optional(),
+    maxDiffBytes: z.number().optional(),
+    mergeMethod: z.enum([
+        'merge',
+        'squash',
+        'rebase'
+    ]).optional(),
+    syncTarget: z.boolean().optional(),
+    scopeRoots: z.string().optional(),
+    workspaceFile: z.string().optional(),
+    cleanNodeModules: z.boolean().optional(),
+    startFrom: z.string().optional(),
+    stopAt: z.string().optional(),
+    script: z.string().optional(),
+    cmd: z.string().optional(),
+    publish: z.boolean().optional(),
+    parallel: z.boolean().optional(),
+    continue: z.boolean().optional(),
+    status: z.boolean().optional(),
+    includeCommitHistory: z.boolean().optional(),
+    includeRecentDiffs: z.boolean().optional(),
+    editorTimeout: z.number().optional(),
+    includeReleaseNotes: z.boolean().optional(),
+    includeGithubIssues: z.boolean().optional(),
+    commitHistoryLimit: z.number().optional(),
+    diffHistoryLimit: z.number().optional(),
+    releaseNotesLimit: z.number().optional(),
+    githubIssuesLimit: z.number().optional(),
+    file: z.string().optional(),
+    directory: z.string().optional(),
+    directories: z.array(z.string()).optional(),
+    externals: z.array(z.string()).optional(),
+    keepTemp: z.boolean().optional(),
+    noMilestones: z.boolean().optional(),
+    subcommand: z.string().optional(),
+    scope: z.string().optional(),
+    tagWorkingBranch: z.boolean().optional(),
+    createRetroactiveTags: z.boolean().optional(),
+    workingTagPrefix: z.string().optional(),
+    updateDeps: z.string().optional(),
+    interProject: z.boolean().optional(),
+    report: z.boolean().optional(),
+    analyze: z.boolean().optional(),
+    strategy: z.enum([
+        'latest',
+        'conservative',
+        'compatible'
+    ]).optional(),
+    selfReflection: z.boolean().optional(),
+    maxAgenticIterations: z.number().optional(),
+    // Pull command options
+    remote: z.string().optional(),
+    branch: z.string().optional(),
+    autoStash: z.boolean().optional(),
+    autoResolve: z.boolean().optional(),
+    // Precommit command options
+    fix: z.boolean().optional()
+});
+// Function to transform flat CLI args into nested Config structure
+const transformCliArgs = (finalCliArgs, commandName)=>{
+    const transformedCliArgs = {};
+    // Root-level properties
+    if (finalCliArgs.dryRun !== undefined) transformedCliArgs.dryRun = finalCliArgs.dryRun;
+    if (finalCliArgs.verbose !== undefined) transformedCliArgs.verbose = finalCliArgs.verbose;
+    if (finalCliArgs.debug !== undefined) transformedCliArgs.debug = finalCliArgs.debug;
+    if (finalCliArgs.model !== undefined) transformedCliArgs.model = finalCliArgs.model;
+    if (finalCliArgs.outputDir !== undefined) transformedCliArgs.outputDirectory = finalCliArgs.outputDir;
+    if (finalCliArgs.preferencesDir !== undefined) transformedCliArgs.preferencesDirectory = finalCliArgs.preferencesDir;
+    if (finalCliArgs.configDir !== undefined) transformedCliArgs.configDirectory = finalCliArgs.configDir;
+    if (finalCliArgs.overrides !== undefined) transformedCliArgs.overrides = finalCliArgs.overrides;
+    if (finalCliArgs.contextDirectories !== undefined) transformedCliArgs.contextDirectories = finalCliArgs.contextDirectories;
+    if (finalCliArgs.openaiReasoning !== undefined) transformedCliArgs.openaiReasoning = finalCliArgs.openaiReasoning;
+    if (finalCliArgs.openaiMaxOutputTokens !== undefined) transformedCliArgs.openaiMaxOutputTokens = finalCliArgs.openaiMaxOutputTokens;
+    // Nested mappings for 'commit' options
+    if (finalCliArgs.add !== undefined || finalCliArgs.cached !== undefined || finalCliArgs.sendit !== undefined || finalCliArgs.skipFileCheck !== undefined || finalCliArgs.maxDiffBytes !== undefined || finalCliArgs.messageLimit !== undefined || finalCliArgs.openaiReasoning !== undefined || finalCliArgs.openaiMaxOutputTokens !== undefined || finalCliArgs.amend !== undefined || finalCliArgs.context !== undefined || finalCliArgs.direction !== undefined || commandName === 'commit' && finalCliArgs.interactive !== undefined || finalCliArgs.push !== undefined) {
+        transformedCliArgs.commit = {};
+        if (finalCliArgs.add !== undefined) transformedCliArgs.commit.add = finalCliArgs.add;
+        if (finalCliArgs.cached !== undefined) transformedCliArgs.commit.cached = finalCliArgs.cached;
+        if (finalCliArgs.sendit !== undefined) transformedCliArgs.commit.sendit = finalCliArgs.sendit;
+        if (finalCliArgs.skipFileCheck !== undefined) transformedCliArgs.commit.skipFileCheck = finalCliArgs.skipFileCheck;
+        if (finalCliArgs.maxDiffBytes !== undefined) transformedCliArgs.commit.maxDiffBytes = finalCliArgs.maxDiffBytes;
+        if (finalCliArgs.messageLimit !== undefined) transformedCliArgs.commit.messageLimit = finalCliArgs.messageLimit;
+        if (finalCliArgs.amend !== undefined) transformedCliArgs.commit.amend = finalCliArgs.amend;
+        if (finalCliArgs.push !== undefined) transformedCliArgs.commit.push = finalCliArgs.push;
+        if (finalCliArgs.context !== undefined) transformedCliArgs.commit.context = finalCliArgs.context;
+        if (finalCliArgs.direction !== undefined) transformedCliArgs.commit.direction = finalCliArgs.direction;
+        if (commandName === 'commit' && finalCliArgs.interactive !== undefined) transformedCliArgs.commit.interactive = finalCliArgs.interactive;
+        if (finalCliArgs.openaiReasoning !== undefined) transformedCliArgs.commit.openaiReasoning = finalCliArgs.openaiReasoning;
+        if (finalCliArgs.openaiMaxOutputTokens !== undefined) transformedCliArgs.commit.openaiMaxOutputTokens = finalCliArgs.openaiMaxOutputTokens;
+    }
+    // Nested mappings for 'audioCommit' options
+    if (finalCliArgs.file !== undefined || finalCliArgs.keepTemp !== undefined || finalCliArgs.openaiReasoning !== undefined || finalCliArgs.openaiMaxOutputTokens !== undefined) {
+        transformedCliArgs.audioCommit = {};
+        if (finalCliArgs.file !== undefined) transformedCliArgs.audioCommit.file = finalCliArgs.file;
+        if (finalCliArgs.keepTemp !== undefined) transformedCliArgs.audioCommit.keepTemp = finalCliArgs.keepTemp;
+        if (finalCliArgs.openaiReasoning !== undefined) transformedCliArgs.audioCommit.openaiReasoning = finalCliArgs.openaiReasoning;
+        if (finalCliArgs.openaiMaxOutputTokens !== undefined) transformedCliArgs.audioCommit.openaiMaxOutputTokens = finalCliArgs.openaiMaxOutputTokens;
+    }
+    // Nested mappings for 'release' options (only when it's NOT a publish command)
+    if (commandName !== 'publish') {
+        if (finalCliArgs.from !== undefined || finalCliArgs.to !== undefined || finalCliArgs.maxDiffBytes !== undefined || finalCliArgs.interactive !== undefined || finalCliArgs.noMilestones !== undefined || finalCliArgs.openaiReasoning !== undefined || finalCliArgs.openaiMaxOutputTokens !== undefined || finalCliArgs.selfReflection !== undefined || finalCliArgs.maxAgenticIterations !== undefined) {
+            transformedCliArgs.release = {};
+            if (finalCliArgs.from !== undefined) transformedCliArgs.release.from = finalCliArgs.from;
+            if (finalCliArgs.to !== undefined) transformedCliArgs.release.to = finalCliArgs.to;
+            if ((commandName === 'release' || finalCliArgs.from !== undefined || finalCliArgs.to !== undefined) && finalCliArgs.context !== undefined) transformedCliArgs.release.context = finalCliArgs.context;
+            if (finalCliArgs.interactive !== undefined) transformedCliArgs.release.interactive = finalCliArgs.interactive;
+            if ((commandName === 'release' || finalCliArgs.from !== undefined || finalCliArgs.to !== undefined) && finalCliArgs.messageLimit !== undefined) transformedCliArgs.release.messageLimit = finalCliArgs.messageLimit;
+            if (finalCliArgs.maxDiffBytes !== undefined) transformedCliArgs.release.maxDiffBytes = finalCliArgs.maxDiffBytes;
+            if (finalCliArgs.noMilestones !== undefined) transformedCliArgs.release.noMilestones = finalCliArgs.noMilestones;
+            if (finalCliArgs.openaiReasoning !== undefined) transformedCliArgs.release.openaiReasoning = finalCliArgs.openaiReasoning;
+            if (finalCliArgs.openaiMaxOutputTokens !== undefined) transformedCliArgs.release.openaiMaxOutputTokens = finalCliArgs.openaiMaxOutputTokens;
+            if (finalCliArgs.selfReflection !== undefined) transformedCliArgs.release.selfReflection = finalCliArgs.selfReflection;
+            if (finalCliArgs.maxAgenticIterations !== undefined) transformedCliArgs.release.maxAgenticIterations = finalCliArgs.maxAgenticIterations;
+        }
+    }
+    // Nested mappings for 'publish' options – map whenever publish-specific options are provided
+    if (finalCliArgs.mergeMethod !== undefined || finalCliArgs.targetVersion !== undefined || finalCliArgs.interactive !== undefined || finalCliArgs.syncTarget !== undefined || finalCliArgs.skipAlreadyPublished !== undefined || finalCliArgs.forceRepublish !== undefined || commandName === 'publish' && (finalCliArgs.from !== undefined || finalCliArgs.noMilestones !== undefined || finalCliArgs.selfReflection !== undefined || finalCliArgs.maxAgenticIterations !== undefined)) {
+        transformedCliArgs.publish = {};
+        if (finalCliArgs.mergeMethod !== undefined) transformedCliArgs.publish.mergeMethod = finalCliArgs.mergeMethod;
+        if ((commandName === 'publish' || finalCliArgs.mergeMethod !== undefined || finalCliArgs.targetVersion !== undefined || finalCliArgs.syncTarget !== undefined || finalCliArgs.interactive !== undefined || finalCliArgs.skipAlreadyPublished !== undefined || finalCliArgs.forceRepublish !== undefined) && finalCliArgs.from !== undefined) transformedCliArgs.publish.from = finalCliArgs.from;
+        if (finalCliArgs.targetVersion !== undefined) transformedCliArgs.publish.targetVersion = finalCliArgs.targetVersion;
+        if (finalCliArgs.interactive !== undefined) transformedCliArgs.publish.interactive = finalCliArgs.interactive;
+        if (finalCliArgs.syncTarget !== undefined) transformedCliArgs.publish.syncTarget = finalCliArgs.syncTarget;
+        if (finalCliArgs.skipAlreadyPublished !== undefined) transformedCliArgs.publish.skipAlreadyPublished = finalCliArgs.skipAlreadyPublished;
+        if (finalCliArgs.forceRepublish !== undefined) transformedCliArgs.publish.forceRepublish = finalCliArgs.forceRepublish;
+        if (finalCliArgs.skipLinkCleanup !== undefined) transformedCliArgs.publish.skipLinkCleanup = finalCliArgs.skipLinkCleanup;
+        if ((commandName === 'publish' || finalCliArgs.mergeMethod !== undefined || finalCliArgs.targetVersion !== undefined || finalCliArgs.syncTarget !== undefined || finalCliArgs.interactive !== undefined || finalCliArgs.skipAlreadyPublished !== undefined || finalCliArgs.forceRepublish !== undefined) && finalCliArgs.noMilestones !== undefined) transformedCliArgs.publish.noMilestones = finalCliArgs.noMilestones;
+        if (finalCliArgs.updateDeps !== undefined) transformedCliArgs.publish.updateDeps = finalCliArgs.updateDeps;
+        // Map release-related flags from publish command into release config (only if any are set)
+        if (commandName === 'publish' && (finalCliArgs.selfReflection !== undefined || finalCliArgs.maxAgenticIterations !== undefined)) {
+            transformedCliArgs.release = {
+                ...transformedCliArgs.release || {},
+                ...finalCliArgs.selfReflection !== undefined ? {
+                    selfReflection: finalCliArgs.selfReflection
+                } : {},
+                ...finalCliArgs.maxAgenticIterations !== undefined ? {
+                    maxAgenticIterations: finalCliArgs.maxAgenticIterations
+                } : {}
+            };
+        }
+    }
+    // Nested mappings for 'development' options
+    if (commandName === 'development' && (finalCliArgs.targetVersion !== undefined || finalCliArgs.noMilestones !== undefined || finalCliArgs.tagWorkingBranch !== undefined || finalCliArgs.createRetroactiveTags !== undefined || finalCliArgs.workingTagPrefix !== undefined)) {
+        transformedCliArgs.development = {};
+        if (finalCliArgs.targetVersion !== undefined) transformedCliArgs.development.targetVersion = finalCliArgs.targetVersion;
+        if (finalCliArgs.noMilestones !== undefined) transformedCliArgs.development.noMilestones = finalCliArgs.noMilestones;
+        if (finalCliArgs.tagWorkingBranch !== undefined) transformedCliArgs.development.tagWorkingBranch = finalCliArgs.tagWorkingBranch;
+        if (finalCliArgs.createRetroactiveTags !== undefined) transformedCliArgs.development.createRetroactiveTags = finalCliArgs.createRetroactiveTags;
+        if (finalCliArgs.workingTagPrefix !== undefined) transformedCliArgs.development.workingTagPrefix = finalCliArgs.workingTagPrefix;
+        // Mirror targetVersion into publish; mirror noMilestones into publish and release to match test expectations
+        transformedCliArgs.publish = {
+            ...transformedCliArgs.publish || {},
+            ...finalCliArgs.targetVersion !== undefined ? {
+                targetVersion: finalCliArgs.targetVersion
+            } : {},
+            ...finalCliArgs.noMilestones !== undefined ? {
+                noMilestones: finalCliArgs.noMilestones
+            } : {}
+        };
+        transformedCliArgs.release = {
+            ...transformedCliArgs.release || {},
+            ...finalCliArgs.noMilestones !== undefined ? {
+                noMilestones: finalCliArgs.noMilestones
+            } : {}
+        };
+    }
+    // Nested mappings for 'link' and 'unlink' options
+    const linkPackageArgument = finalCliArgs.packageArgument;
+    if ((commandName === 'link' || commandName === undefined) && (finalCliArgs.scopeRoots !== undefined || linkPackageArgument !== undefined)) {
+        transformedCliArgs.link = {};
+        if (finalCliArgs.scopeRoots !== undefined) {
+            try {
+                transformedCliArgs.link.scopeRoots = safeJsonParse(finalCliArgs.scopeRoots, 'scopeRoots CLI argument');
+            } catch (error) {
+                throw new Error(`Invalid JSON for scope-roots: ${finalCliArgs.scopeRoots}`);
+            }
+        }
+        if (linkPackageArgument !== undefined) {
+            transformedCliArgs.link.packageArgument = linkPackageArgument;
+        }
+    }
+    // Nested mappings for 'unlink' options
+    const unlinkPackageArgument = finalCliArgs.packageArgument;
+    if (commandName === 'unlink' && (finalCliArgs.scopeRoots !== undefined || unlinkPackageArgument !== undefined || finalCliArgs.workspaceFile !== undefined || finalCliArgs.cleanNodeModules !== undefined)) {
+        transformedCliArgs.unlink = {};
+        if (finalCliArgs.scopeRoots !== undefined) {
+            try {
+                transformedCliArgs.unlink.scopeRoots = safeJsonParse(finalCliArgs.scopeRoots, 'scopeRoots CLI argument');
+            } catch (error) {
+                throw new Error(`Invalid JSON for scope-roots: ${finalCliArgs.scopeRoots}`);
+            }
+        }
+        if (finalCliArgs.workspaceFile !== undefined) transformedCliArgs.unlink.workspaceFile = finalCliArgs.workspaceFile;
+        if (finalCliArgs.cleanNodeModules !== undefined) transformedCliArgs.unlink.cleanNodeModules = finalCliArgs.cleanNodeModules;
+        if (unlinkPackageArgument !== undefined) {
+            transformedCliArgs.unlink.packageArgument = unlinkPackageArgument;
+        }
+    }
+    // Nested mappings for 'audio-review' options (only when it's not a tree command)
+    if (commandName !== 'tree' && (finalCliArgs.includeCommitHistory !== undefined || finalCliArgs.includeRecentDiffs !== undefined || finalCliArgs.includeReleaseNotes !== undefined || finalCliArgs.includeGithubIssues !== undefined || finalCliArgs.commitHistoryLimit !== undefined || finalCliArgs.diffHistoryLimit !== undefined || finalCliArgs.releaseNotesLimit !== undefined || finalCliArgs.githubIssuesLimit !== undefined || finalCliArgs.file !== undefined || finalCliArgs.directories !== undefined || finalCliArgs.keepTemp !== undefined || finalCliArgs.openaiReasoning !== undefined || finalCliArgs.openaiMaxOutputTokens !== undefined)) {
+        transformedCliArgs.audioReview = {};
+        if (finalCliArgs.includeCommitHistory !== undefined) transformedCliArgs.audioReview.includeCommitHistory = finalCliArgs.includeCommitHistory;
+        if (finalCliArgs.includeRecentDiffs !== undefined) transformedCliArgs.audioReview.includeRecentDiffs = finalCliArgs.includeRecentDiffs;
+        if (finalCliArgs.includeReleaseNotes !== undefined) transformedCliArgs.audioReview.includeReleaseNotes = finalCliArgs.includeReleaseNotes;
+        if (finalCliArgs.includeGithubIssues !== undefined) transformedCliArgs.audioReview.includeGithubIssues = finalCliArgs.includeGithubIssues;
+        if (finalCliArgs.commitHistoryLimit !== undefined) transformedCliArgs.audioReview.commitHistoryLimit = finalCliArgs.commitHistoryLimit;
+        if (finalCliArgs.diffHistoryLimit !== undefined) transformedCliArgs.audioReview.diffHistoryLimit = finalCliArgs.diffHistoryLimit;
+        if (finalCliArgs.releaseNotesLimit !== undefined) transformedCliArgs.audioReview.releaseNotesLimit = finalCliArgs.releaseNotesLimit;
+        if (finalCliArgs.githubIssuesLimit !== undefined) transformedCliArgs.audioReview.githubIssuesLimit = finalCliArgs.githubIssuesLimit;
+        if (finalCliArgs.context !== undefined) transformedCliArgs.audioReview.context = finalCliArgs.context;
+        if (finalCliArgs.sendit !== undefined) transformedCliArgs.audioReview.sendit = finalCliArgs.sendit;
+        if (finalCliArgs.file !== undefined) transformedCliArgs.audioReview.file = finalCliArgs.file;
+        if (finalCliArgs.directory !== undefined) transformedCliArgs.audioReview.directory = finalCliArgs.directory;
+        if (finalCliArgs.keepTemp !== undefined) transformedCliArgs.audioReview.keepTemp = finalCliArgs.keepTemp;
+        if (finalCliArgs.openaiReasoning !== undefined) transformedCliArgs.audioReview.openaiReasoning = finalCliArgs.openaiReasoning;
+        if (finalCliArgs.openaiMaxOutputTokens !== undefined) transformedCliArgs.audioReview.openaiMaxOutputTokens = finalCliArgs.openaiMaxOutputTokens;
+    }
+    // Nested mappings for 'precommit' options
+    if (finalCliArgs.fix !== undefined) {
+        transformedCliArgs.precommit = {};
+        transformedCliArgs.precommit.fix = finalCliArgs.fix;
+    }
+    // Nested mappings for 'review' options
+    if (finalCliArgs.includeCommitHistory !== undefined || finalCliArgs.includeRecentDiffs !== undefined || finalCliArgs.includeReleaseNotes !== undefined || finalCliArgs.includeGithubIssues !== undefined || finalCliArgs.commitHistoryLimit !== undefined || finalCliArgs.diffHistoryLimit !== undefined || finalCliArgs.releaseNotesLimit !== undefined || finalCliArgs.githubIssuesLimit !== undefined || finalCliArgs.context !== undefined || finalCliArgs.sendit !== undefined || finalCliArgs.note !== undefined || finalCliArgs.openaiReasoning !== undefined || finalCliArgs.openaiMaxOutputTokens !== undefined || commandName === 'review' && (finalCliArgs.file !== undefined || finalCliArgs.directory !== undefined)) {
+        transformedCliArgs.review = {};
+        if (finalCliArgs.note !== undefined) transformedCliArgs.review.note = finalCliArgs.note;
+        if (commandName === 'review' && finalCliArgs.file !== undefined) transformedCliArgs.review.file = finalCliArgs.file;
+        if (commandName === 'review' && finalCliArgs.directory !== undefined) transformedCliArgs.review.directory = finalCliArgs.directory;
+        // Include optional review configuration options if specified
+        if (finalCliArgs.includeCommitHistory !== undefined) transformedCliArgs.review.includeCommitHistory = finalCliArgs.includeCommitHistory;
+        if (finalCliArgs.includeRecentDiffs !== undefined) transformedCliArgs.review.includeRecentDiffs = finalCliArgs.includeRecentDiffs;
+        if (finalCliArgs.includeReleaseNotes !== undefined) transformedCliArgs.review.includeReleaseNotes = finalCliArgs.includeReleaseNotes;
+        if (finalCliArgs.includeGithubIssues !== undefined) transformedCliArgs.review.includeGithubIssues = finalCliArgs.includeGithubIssues;
+        if (finalCliArgs.commitHistoryLimit !== undefined) transformedCliArgs.review.commitHistoryLimit = finalCliArgs.commitHistoryLimit;
+        if (finalCliArgs.diffHistoryLimit !== undefined) transformedCliArgs.review.diffHistoryLimit = finalCliArgs.diffHistoryLimit;
+        if (finalCliArgs.releaseNotesLimit !== undefined) transformedCliArgs.review.releaseNotesLimit = finalCliArgs.releaseNotesLimit;
+        if (finalCliArgs.githubIssuesLimit !== undefined) transformedCliArgs.review.githubIssuesLimit = finalCliArgs.githubIssuesLimit;
+        if (finalCliArgs.context !== undefined) transformedCliArgs.review.context = finalCliArgs.context;
+        if (finalCliArgs.sendit !== undefined) transformedCliArgs.review.sendit = finalCliArgs.sendit;
+        if (finalCliArgs.editorTimeout !== undefined) transformedCliArgs.review.editorTimeout = finalCliArgs.editorTimeout;
+        if (finalCliArgs.openaiReasoning !== undefined) transformedCliArgs.review.openaiReasoning = finalCliArgs.openaiReasoning;
+        if (finalCliArgs.openaiMaxOutputTokens !== undefined) transformedCliArgs.review.openaiMaxOutputTokens = finalCliArgs.openaiMaxOutputTokens;
+    }
+    // Nested mappings for 'tree' options (add when relevant args present)
+    if (commandName === 'tree') {
+        const builtInCommand = finalCliArgs.builtInCommand;
+        const packageArgument = finalCliArgs.packageArgument;
+        // Map command-specific options to nested configs for tree operations
+        // When tree commit/release/publish is run, these options get forwarded
+        if (builtInCommand === 'commit' && finalCliArgs.contextFiles !== undefined) {
+            if (!transformedCliArgs.commit) transformedCliArgs.commit = {};
+            transformedCliArgs.commit.contextFiles = finalCliArgs.contextFiles;
+        }
+        if (builtInCommand === 'commit' && finalCliArgs.selfReflection !== undefined) {
+            if (!transformedCliArgs.commit) transformedCliArgs.commit = {};
+            transformedCliArgs.commit.selfReflection = finalCliArgs.selfReflection;
+        }
+        if (builtInCommand === 'commit' && finalCliArgs.maxAgenticIterations !== undefined) {
+            if (!transformedCliArgs.commit) transformedCliArgs.commit = {};
+            transformedCliArgs.commit.maxAgenticIterations = finalCliArgs.maxAgenticIterations;
+        }
+        if ((builtInCommand === 'release' || builtInCommand === 'publish') && finalCliArgs.contextFiles !== undefined) {
+            if (!transformedCliArgs.release) transformedCliArgs.release = {};
+            transformedCliArgs.release.contextFiles = finalCliArgs.contextFiles;
+        }
+        if ((builtInCommand === 'release' || builtInCommand === 'publish') && finalCliArgs.selfReflection !== undefined) {
+            if (!transformedCliArgs.release) transformedCliArgs.release = {};
+            transformedCliArgs.release.selfReflection = finalCliArgs.selfReflection;
+        }
+        if ((builtInCommand === 'release' || builtInCommand === 'publish') && finalCliArgs.maxAgenticIterations !== undefined) {
+            if (!transformedCliArgs.release) transformedCliArgs.release = {};
+            transformedCliArgs.release.maxAgenticIterations = finalCliArgs.maxAgenticIterations;
+        }
+        // Only create tree object if there are actual tree-specific options
+        const cliArgs = finalCliArgs;
+        if (finalCliArgs.directories !== undefined || finalCliArgs.directory !== undefined || finalCliArgs.startFrom !== undefined || finalCliArgs.stopAt !== undefined || finalCliArgs.cmd !== undefined || builtInCommand !== undefined || finalCliArgs.continue !== undefined || packageArgument !== undefined || finalCliArgs.cleanNodeModules !== undefined || finalCliArgs.externals !== undefined || cliArgs.statusParallel !== undefined || cliArgs.auditBranches !== undefined || cliArgs.parallel !== undefined || cliArgs.markCompleted !== undefined || cliArgs.skip !== undefined || cliArgs.retryFailed !== undefined || cliArgs.skipFailed !== undefined || cliArgs.validateState !== undefined || cliArgs.order !== undefined) {
+            transformedCliArgs.tree = {};
+            if (finalCliArgs.directories !== undefined) transformedCliArgs.tree.directories = finalCliArgs.directories;
+            else if (finalCliArgs.directory !== undefined) transformedCliArgs.tree.directories = [
+                finalCliArgs.directory
+            ];
+            if (finalCliArgs.startFrom !== undefined) transformedCliArgs.tree.startFrom = finalCliArgs.startFrom;
+            if (finalCliArgs.stopAt !== undefined) transformedCliArgs.tree.stopAt = finalCliArgs.stopAt;
+            if (finalCliArgs.cmd !== undefined) transformedCliArgs.tree.cmd = finalCliArgs.cmd;
+            // Note: parallel property is not part of the tree config type
+            if (builtInCommand !== undefined) transformedCliArgs.tree.builtInCommand = builtInCommand;
+            if (finalCliArgs.continue !== undefined) transformedCliArgs.tree.continue = finalCliArgs.continue;
+            if (finalCliArgs.status !== undefined) transformedCliArgs.tree.status = finalCliArgs.status;
+            if (packageArgument !== undefined) transformedCliArgs.tree.packageArgument = packageArgument;
+            if (finalCliArgs.cleanNodeModules !== undefined) transformedCliArgs.tree.cleanNodeModules = finalCliArgs.cleanNodeModules;
+            if (finalCliArgs.externals !== undefined) transformedCliArgs.tree.externals = finalCliArgs.externals;
+            // Parallel execution options
+            if (cliArgs.parallel !== undefined) transformedCliArgs.tree.parallel = cliArgs.parallel;
+            if (cliArgs.maxConcurrency !== undefined) transformedCliArgs.tree.maxConcurrency = cliArgs.maxConcurrency;
+            if (cliArgs.maxRetries !== undefined || cliArgs.retryDelay !== undefined) {
+                transformedCliArgs.tree.retry = {
+                    maxAttempts: cliArgs.maxRetries || 3,
+                    initialDelayMs: cliArgs.retryDelay || 5000,
+                    maxDelayMs: 60000,
+                    backoffMultiplier: 2
+                };
+            }
+            // Recovery options
+            if (cliArgs.statusParallel !== undefined) transformedCliArgs.tree.statusParallel = cliArgs.statusParallel;
+            if (cliArgs.auditBranches !== undefined) transformedCliArgs.tree.auditBranches = cliArgs.auditBranches;
+            if (cliArgs.markCompleted !== undefined) {
+                transformedCliArgs.tree.markCompleted = cliArgs.markCompleted.split(',').map((s)=>s.trim());
+            }
+            if (cliArgs.skip !== undefined) {
+                transformedCliArgs.tree.skipPackages = cliArgs.skip.split(',').map((s)=>s.trim());
+            }
+            if (cliArgs.retryFailed !== undefined) transformedCliArgs.tree.retryFailed = cliArgs.retryFailed;
+            if (cliArgs.skipFailed !== undefined) transformedCliArgs.tree.skipFailed = cliArgs.skipFailed;
+            if (cliArgs.validateState !== undefined) transformedCliArgs.tree.validateState = cliArgs.validateState;
+            if (cliArgs.order !== undefined) transformedCliArgs.tree.order = cliArgs.order;
+        }
+    }
+    // Nested mappings for 'development' options
+    if (commandName === 'development' && (finalCliArgs.targetVersion !== undefined || finalCliArgs.noMilestones !== undefined || finalCliArgs.tagWorkingBranch !== undefined || finalCliArgs.createRetroactiveTags !== undefined || finalCliArgs.workingTagPrefix !== undefined)) {
+        transformedCliArgs.development = {};
+        if (finalCliArgs.targetVersion !== undefined) transformedCliArgs.development.targetVersion = finalCliArgs.targetVersion;
+        if (finalCliArgs.noMilestones !== undefined) transformedCliArgs.development.noMilestones = finalCliArgs.noMilestones;
+        if (finalCliArgs.tagWorkingBranch !== undefined) transformedCliArgs.development.tagWorkingBranch = finalCliArgs.tagWorkingBranch;
+        if (finalCliArgs.createRetroactiveTags !== undefined) transformedCliArgs.development.createRetroactiveTags = finalCliArgs.createRetroactiveTags;
+        if (finalCliArgs.workingTagPrefix !== undefined) transformedCliArgs.development.workingTagPrefix = finalCliArgs.workingTagPrefix;
+    }
+    // Nested mappings for 'versions' options
+    if (commandName === 'versions' && (finalCliArgs.subcommand !== undefined || finalCliArgs.directories !== undefined)) {
+        transformedCliArgs.versions = {};
+        if (finalCliArgs.subcommand !== undefined) transformedCliArgs.versions.subcommand = finalCliArgs.subcommand;
+        if (finalCliArgs.directories !== undefined) transformedCliArgs.versions.directories = finalCliArgs.directories;
+    }
+    // Nested mappings for 'updates' options
+    if (commandName === 'updates' && (finalCliArgs.scope !== undefined || finalCliArgs.directories !== undefined || finalCliArgs.interProject !== undefined || finalCliArgs.report !== undefined || finalCliArgs.analyze !== undefined || finalCliArgs.strategy !== undefined)) {
+        transformedCliArgs.updates = {};
+        if (finalCliArgs.scope !== undefined) transformedCliArgs.updates.scope = finalCliArgs.scope;
+        if (finalCliArgs.directories !== undefined) transformedCliArgs.updates.directories = finalCliArgs.directories;
+        if (finalCliArgs.interProject !== undefined) transformedCliArgs.updates.interProject = finalCliArgs.interProject;
+        if (finalCliArgs.report !== undefined) transformedCliArgs.updates.report = finalCliArgs.report;
+        if (finalCliArgs.analyze !== undefined) transformedCliArgs.updates.analyze = finalCliArgs.analyze;
+        if (finalCliArgs.strategy !== undefined) transformedCliArgs.updates.strategy = finalCliArgs.strategy;
+    }
+    // Nested mappings for 'pull' options
+    if (commandName === 'pull' && (finalCliArgs.remote !== undefined || finalCliArgs.branch !== undefined || finalCliArgs.autoStash !== undefined || finalCliArgs.autoResolve !== undefined)) {
+        transformedCliArgs.pull = {};
+        if (finalCliArgs.remote !== undefined) transformedCliArgs.pull.remote = finalCliArgs.remote;
+        if (finalCliArgs.branch !== undefined) transformedCliArgs.pull.branch = finalCliArgs.branch;
+        if (finalCliArgs.autoStash !== undefined) transformedCliArgs.pull.autoStash = finalCliArgs.autoStash;
+        if (finalCliArgs.autoResolve !== undefined) transformedCliArgs.pull.autoResolve = finalCliArgs.autoResolve;
+    }
+    // Handle excluded patterns (Commander.js converts --excluded-paths to excludedPaths)
+    // Also handle exclude as alias for excludedPatterns
+    const excludedPatterns = finalCliArgs.excludedPatterns || finalCliArgs.exclude || finalCliArgs.excludedPaths;
+    if (excludedPatterns !== undefined) {
+        if (commandName === 'tree') {
+            // For tree command, map to both root level excludedPatterns AND tree.exclude
+            transformedCliArgs.excludedPatterns = excludedPatterns;
+            if (!transformedCliArgs.tree) {
+                transformedCliArgs.tree = {};
+            }
+            transformedCliArgs.tree.exclude = excludedPatterns;
+        } else {
+            // For non-tree commands, map to root level excludedPatterns
+            transformedCliArgs.excludedPatterns = excludedPatterns;
+        }
+    }
+    // Handle externals - map to appropriate command objects based on command type
+    if (finalCliArgs.externals !== undefined) {
+        if (commandName === 'link') {
+            if (!transformedCliArgs.link) {
+                transformedCliArgs.link = {};
+            }
+            transformedCliArgs.link.externals = finalCliArgs.externals;
+        } else if (commandName === 'unlink') {
+            if (!transformedCliArgs.unlink) {
+                transformedCliArgs.unlink = {};
+            }
+            transformedCliArgs.unlink.externals = finalCliArgs.externals;
+        } else if (commandName === 'tree') {
+            if (!transformedCliArgs.tree) {
+                transformedCliArgs.tree = {};
+            }
+            transformedCliArgs.tree.externals = finalCliArgs.externals;
+        }
+    }
+    // Note: openaiApiKey is handled separately via environment variable only
+    return transformedCliArgs;
+};
+// Update configure signature to accept cardigantime
+const configure = async (cardigantime)=>{
+    var _config_contextDirectories, _config_link;
+    const logger = getLogger();
+    let program = new Command();
+    // Configure program basics with custom version string
+    const versionString = `${VERSION}\nBuilt on: ${BUILD_HOSTNAME}\nBuild time: ${BUILD_TIMESTAMP}`;
+    program.name(PROGRAM_NAME).summary('Create Intelligent Release Notes or Change Logs from Git').description('Create Intelligent Release Notes or Change Logs from Git').version(versionString, '-V, --version', 'Display version information');
+    // Let cardigantime add its arguments first
+    program = await cardigantime.configure(program);
+    // Check if --check-config is in process.argv early
+    if (process.argv.includes('--check-config')) {
+        // For check-config, use CardiganTime's built-in checkConfig method
+        program.parse();
+        const cliArgs = program.opts();
+        // Transform the flat CLI args
+        const transformedCliArgs = transformCliArgs(cliArgs);
+        // Use CardiganTime's built-in checkConfig method which displays
+        // hierarchical configuration information in a well-formatted way
+        await cardigantime.checkConfig(transformedCliArgs);
+        // Return minimal config for consistency, but main processing is done
+        const config = await validateAndProcessOptions({});
+        const secureConfig = await validateAndProcessSecureOptions();
+        const commandConfig = {
+            commandName: 'check-config'
+        };
+        return [
+            config,
+            secureConfig,
+            commandConfig
+        ];
+    }
+    // Check if --init-config is in process.argv early
+    if (process.argv.includes('--init-config')) {
+        // For init-config, use CardiganTime's built-in generateConfig method
+        program.parse();
+        const cliArgs = program.opts();
+        // Transform the flat CLI args
+        const transformedCliArgs = transformCliArgs(cliArgs);
+        // Use CardiganTime's built-in generateConfig method
+        const configDir = transformedCliArgs.configDirectory || KODRDRIV_DEFAULTS.configDirectory;
+        const absoluteConfigDir = path.isAbsolute(configDir) ? configDir : path.resolve(process.cwd(), configDir);
+        await cardigantime.generateConfig(absoluteConfigDir);
+        // Return minimal config for consistency, but main processing is done
+        const config = await validateAndProcessOptions({});
+        const secureConfig = await validateAndProcessSecureOptions();
+        const commandConfig = {
+            commandName: 'init-config'
+        };
+        return [
+            config,
+            secureConfig,
+            commandConfig
+        ];
+    }
+    // Get CLI arguments using the new function
+    const [finalCliArgs, commandConfig] = await getCliConfig(program);
+    logger.silly('Loaded Command Line Options: %s', JSON.stringify(finalCliArgs, null, 2));
+    // Transform the flat CLI args using the new function
+    const transformedCliArgs = transformCliArgs(finalCliArgs, commandConfig.commandName);
+    logger.silly('Transformed CLI Args for merging: %s', JSON.stringify(transformedCliArgs, null, 2));
+    // Get values from config file using Cardigantime's hierarchical configuration
+    const fileValues = await cardigantime.read(transformedCliArgs);
+    // Merge configurations: Defaults -> File -> CLI
+    // Properly merge nested sections to preserve config file values when CLI args are partial
+    const mergedLink = {
+        ...KODRDRIV_DEFAULTS.link,
+        ...fileValues.link,
+        ...transformedCliArgs.link
+    };
+    const mergedCommit = {
+        ...KODRDRIV_DEFAULTS.commit,
+        ...fileValues.commit,
+        ...transformedCliArgs.commit
+    };
+    const mergedRelease = {
+        ...KODRDRIV_DEFAULTS.release,
+        ...fileValues.release,
+        ...transformedCliArgs.release
+    };
+    const mergedPublish = {
+        ...KODRDRIV_DEFAULTS.publish,
+        ...fileValues.publish,
+        ...transformedCliArgs.publish
+    };
+    const mergedAudioCommit = {
+        ...KODRDRIV_DEFAULTS.audioCommit,
+        ...fileValues.audioCommit,
+        ...transformedCliArgs.audioCommit
+    };
+    const mergedAudioReview = {
+        ...KODRDRIV_DEFAULTS.audioReview,
+        ...fileValues.audioReview,
+        ...transformedCliArgs.audioReview
+    };
+    const mergedReview = {
+        ...KODRDRIV_DEFAULTS.review,
+        ...fileValues.review,
+        ...transformedCliArgs.review
+    };
+    const mergedTree = {
+        ...KODRDRIV_DEFAULTS.tree,
+        ...fileValues.tree,
+        ...transformedCliArgs.tree
+    };
+    const mergedBranches = {
+        ...KODRDRIV_DEFAULTS.branches || {},
+        ...fileValues.branches || {},
+        ...transformedCliArgs.branches || {}
+    };
+    const mergedVersions = {
+        ...KODRDRIV_DEFAULTS.versions,
+        ...fileValues.versions,
+        ...transformedCliArgs.versions
+    };
+    const mergedUpdates = {
+        ...KODRDRIV_DEFAULTS.updates,
+        ...fileValues.updates,
+        ...transformedCliArgs.updates
+    };
+    const partialConfig = {
+        ...KODRDRIV_DEFAULTS,
+        ...fileValues,
+        ...transformedCliArgs,
+        // Override with properly merged nested sections
+        link: mergedLink,
+        commit: mergedCommit,
+        release: mergedRelease,
+        publish: mergedPublish,
+        audioCommit: mergedAudioCommit,
+        audioReview: mergedAudioReview,
+        review: mergedReview,
+        tree: mergedTree,
+        branches: mergedBranches,
+        versions: mergedVersions,
+        updates: mergedUpdates
+    }; // Cast to Partial<Config> initially
+    // Specific validation and processing after merge
+    const config = await validateAndProcessOptions(partialConfig);
+    // Log effective configuration summary at verbose level
+    logger.verbose('Configuration complete. Effective settings:');
+    logger.verbose(`  Command: ${commandConfig.commandName}`);
+    logger.verbose(`  Model: ${config.model}`);
+    logger.verbose(`  Dry run: ${config.dryRun}`);
+    logger.verbose(`  Debug: ${config.debug}`);
+    logger.verbose(`  Verbose: ${config.verbose}`);
+    logger.verbose(`  Config directory: ${config.configDirectory}`);
+    logger.verbose(`  Output directory: ${config.outputDirectory}`);
+    logger.verbose(`  Context directories: ${((_config_contextDirectories = config.contextDirectories) === null || _config_contextDirectories === void 0 ? void 0 : _config_contextDirectories.join(', ')) || 'none'}`);
+    if (config.excludedPatterns && config.excludedPatterns.length > 0) {
+        logger.verbose(`  Excluded patterns: ${config.excludedPatterns.join(', ')}`);
+    }
+    if (Object.keys(((_config_link = config.link) === null || _config_link === void 0 ? void 0 : _config_link.scopeRoots) || {}).length > 0) {
+        logger.verbose(`  Link scope roots: ${Object.keys(config.link.scopeRoots).join(', ')}`);
+    }
+    logger.silly('Final configuration: %s', JSON.stringify(config, null, 2));
+    const secureConfig = await validateAndProcessSecureOptions();
+    return [
+        config,
+        secureConfig,
+        commandConfig
+    ];
+};
+// Function to handle CLI argument parsing and processing
+async function getCliConfig(program, commands) {
+    const addSharedOptions = (command)=>{
+        command.option('--dry-run', 'perform a dry run without saving files') // Removed default, will be handled by merging
+        .option('--verbose', 'enable verbose logging').option('--debug', 'enable debug logging').option('--overrides', 'enable overrides').option('--model <model>', 'OpenAI model to use').option('--openai-reasoning <level>', 'OpenAI reasoning level (low, medium, high)').option('--openai-max-output-tokens <tokens>', 'OpenAI maximum output tokens', parseInt).option('-d, --context-directories [contextDirectories...]', 'directories to scan for context').option('--config-dir <configDir>', 'configuration directory') // Keep config-dir for specifying location
+        .option('--output-dir <outputDir>', 'output directory for generated files').option('--preferences-dir <preferencesDir>', 'preferences directory for personal settings').option('--excluded-paths [excludedPatterns...]', 'paths to exclude from the diff').option('--keep-temp', 'keep temporary recording files');
+    };
+    // Add global options to the main program
+    // (cardigantime already adds most global options like --verbose, --debug, --config-dir)
+    // Add subcommands
+    const commitCommand = program.command('commit').argument('[direction]', 'direction or guidance for the commit message').description('Generate commit notes').option('--context <context>', 'context for the commit message').option('--context-files [contextFiles...]', 'files containing additional context for the commit message').option('--cached', 'use cached diff').option('--add', 'add all changes before committing').option('--sendit', 'Commit with the message generated. No review.').option('--interactive', 'Present commit message for interactive review and editing').option('--amend', 'Amend the last commit with the generated message').option('--push [remote]', 'push to remote after committing (default: origin)').option('--message-limit <messageLimit>', 'limit the number of messages to generate').option('--skip-file-check', 'skip check for file: dependencies before committing').option('--max-diff-bytes <maxDiffBytes>', 'maximum bytes per file in diff (default: 2048)').option('--self-reflection', 'generate self-reflection report with tool effectiveness analysis').option('--max-agentic-iterations <iterations>', 'maximum iterations for analysis (default: 10)', parseInt).option('--allow-commit-splitting', 'allow AI to suggest splitting commits').option('--tool-timeout <timeout>', 'timeout for tool execution in milliseconds', parseInt);
+    // Add shared options to commit command
+    addSharedOptions(commitCommand);
+    // Customize help output for commit command
+    commitCommand.configureHelp({
+        formatHelp: (cmd, helper)=>{
+            const nameAndVersion = `${helper.commandUsage(cmd)}\n\n${helper.commandDescription(cmd)}\n`;
+            const commitOptions = [
+                [
+                    '--context <context>',
+                    'context for the commit message'
+                ],
+                [
+                    '--context-files [contextFiles...]',
+                    'files containing additional context'
+                ]
+            ];
+            const behavioralOptions = [
+                [
+                    '--cached',
+                    'use cached diff'
+                ],
+                [
+                    '--add',
+                    'add all changes before committing'
+                ],
+                [
+                    '--sendit',
+                    'Commit with the message generated. No review.'
+                ],
+                [
+                    '--interactive',
+                    'Present commit message for interactive review and editing'
+                ],
+                [
+                    '--amend',
+                    'Amend the last commit with the generated message'
+                ],
+                [
+                    '--push [remote]',
+                    'push to remote after committing (default: origin)'
+                ],
+                [
+                    '--message-limit <messageLimit>',
+                    'limit the number of messages to generate'
+                ],
+                [
+                    '--skip-file-check',
+                    'skip check for file: dependencies before committing'
+                ],
+                [
+                    '--max-diff-bytes <maxDiffBytes>',
+                    'maximum bytes per file in diff (default: 20480)'
+                ]
+            ];
+            const aiOptions = [
+                [
+                    '--self-reflection',
+                    'generate self-reflection report with tool effectiveness analysis'
+                ],
+                [
+                    '--max-agentic-iterations <iterations>',
+                    'maximum iterations for AI analysis (default: 10)'
+                ],
+                [
+                    '--allow-commit-splitting',
+                    'allow AI to suggest splitting commits'
+                ],
+                [
+                    '--tool-timeout <timeout>',
+                    'timeout for tool execution in milliseconds'
+                ]
+            ];
+            const globalOptions = [
+                [
+                    '--dry-run',
+                    'perform a dry run without saving files'
+                ],
+                [
+                    '--verbose',
+                    'enable verbose logging'
+                ],
+                [
+                    '--debug',
+                    'enable debug logging'
+                ],
+                [
+                    '--overrides',
+                    'enable overrides'
+                ],
+                [
+                    '--model <model>',
+                    'OpenAI model to use'
+                ],
+                [
+                    '--openai-reasoning <level>',
+                    'OpenAI reasoning level (low, medium, high)'
+                ],
+                [
+                    '--openai-max-output-tokens <tokens>',
+                    'OpenAI maximum output tokens'
+                ],
+                [
+                    '-d, --context-directories [contextDirectories...]',
+                    'directories to scan for context'
+                ],
+                [
+                    '--config-dir <configDir>',
+                    'configuration directory'
+                ],
+                [
+                    '--excluded-paths [excludedPatterns...]',
+                    'paths to exclude from the diff'
+                ],
+                [
+                    '-h, --help',
+                    'display help for command'
+                ]
+            ];
+            const formatOptionsSection = (title, options)=>{
+                const maxWidth = Math.max(...options.map(([flag])=>flag.length));
+                return `${title}:\n` + options.map(([flag, desc])=>`  ${flag.padEnd(maxWidth + 2)} ${desc}`).join('\n') + '\n';
+            };
+            return nameAndVersion + '\n' + formatOptionsSection('Commit Message Options', commitOptions) + '\n' + formatOptionsSection('Behavioral Options', behavioralOptions) + '\n' + formatOptionsSection('AI Options', aiOptions) + '\n' + formatOptionsSection('Global Options', globalOptions) + '\n' + 'Environment Variables:\n' + '  OPENAI_API_KEY          OpenAI API key (required)\n';
+        }
+    });
+    const audioCommitCommand = program.command('audio-commit').option('--cached', 'use cached diff').option('--add', 'add all changes before committing').option('--sendit', 'Commit with the message generated. No review.').option('--direction <direction>', 'direction or guidance for the commit message').option('--message-limit <messageLimit>', 'limit the number of messages to generate').option('--file <file>', 'audio file path').description('Record audio to provide context, then generate and optionally commit with AI-generated message');
+    addSharedOptions(audioCommitCommand);
+    const releaseCommand = program.command('release').option('--from <from>', 'branch to generate release notes from').option('--to <to>', 'branch to generate release notes to').option('--context <context>', 'context for the commit message').option('--context-files [contextFiles...]', 'files containing additional context for release notes').option('--interactive', 'Present release notes for interactive review and editing').option('--max-diff-bytes <maxDiffBytes>', 'maximum bytes per file in diff (default: 2048)').option('--no-milestones', 'disable GitHub milestone integration').option('--from-main', 'force comparison against main branch instead of previous release tag').option('--self-reflection', 'generate self-reflection report with tool effectiveness analysis').option('--max-agentic-iterations <maxAgenticIterations>', 'maximum iterations for analysis (default: 30)', parseInt).description('Generate release notes');
+    addSharedOptions(releaseCommand);
+    const publishCommand = program.command('publish').option('--merge-method <method>', 'method to merge PR (merge, squash, rebase)', 'squash').option('--from <from>', 'branch/tag to generate release notes from (default: previous release tag)').option('--target-version <targetVersion>', 'target version for release (explicit version like "4.30.0" or semantic bump: "patch", "minor", "major")').option('--context-files [contextFiles...]', 'files containing additional context for release notes').option('--interactive', 'present release notes for interactive review and editing').option('--sendit', 'skip all confirmation prompts and proceed automatically').option('--sync-target', 'attempt to automatically sync target branch with remote before publishing').option('--skip-already-published', 'skip packages that are already published at target version on npm').option('--force-republish', 'delete existing tags and force republish even if tag exists').option('--no-milestones', 'disable GitHub milestone integration').option('--from-main', 'force comparison against main branch instead of previous release tag').option('--update-deps <scope>', 'update inter-project dependencies before publish (e.g., --update-deps @fjell)').option('--self-reflection', 'generate self-reflection report with tool effectiveness analysis').option('--max-agentic-iterations <maxAgenticIterations>', 'maximum iterations for analysis (default: 30)', parseInt).option('--agentic-publish', 'use AI agent to automatically diagnose and fix publish issues').option('--agentic-publish-max-iterations <agenticPublishMaxIterations>', 'maximum iterations for agentic publish (default: 10)', parseInt).description('Publish a release');
+    addSharedOptions(publishCommand);
+    const treeCommand = program.command('tree [command] [packageArgument]').option('--directory <directory>', 'target directory containing multiple packages (defaults to current directory)').option('--directories [directories...]', 'target directories containing multiple packages (defaults to current directory)').option('--start-from <startFrom>', 'resume execution from this package directory name (useful for restarting failed builds)').option('--stop-at <stopAt>', 'stop execution at this package directory name (the specified package will not be executed)').option('--cmd <cmd>', 'shell command to execute in each package directory (e.g., "npm install", "git status")')// Parallel Execution Options
+    .option('--parallel', 'execute packages in parallel when dependencies allow (packages with no interdependencies run simultaneously)').option('--max-concurrency <number>', 'maximum number of packages to execute concurrently (default: number of CPU cores)', parseInt).option('--max-retries <number>', 'maximum retry attempts for failed packages (default: 3)', parseInt).option('--retry-delay <ms>', 'initial retry delay in milliseconds (default: 5000)', parseInt)// Recovery & Status Options
+    .option('--continue', 'continue from previous tree publish execution using saved checkpoint state').option('--status', 'check status of running tree publish processes').option('--status-parallel', 'show detailed parallel execution status with package states, timing, and errors').option('--audit-branches', 'audit git branch state across all packages (checks branch consistency, merge conflicts with target, existing PRs, sync status, unpushed commits)').option('--promote <packageName>', 'mark a package as completed in the execution context (useful for recovery after timeouts)').option('--mark-completed <packages>', 'mark packages as completed using directory names (comma-separated, for recovery)').option('--skip <packages>', 'skip packages and their dependents (comma-separated)').option('--retry-failed', 'retry all previously failed packages from checkpoint').option('--skip-failed', 'skip failed packages and continue with remaining packages').option('--validate-state', 'validate checkpoint state integrity before continuing').option('--order', 'show package execution order (topological sort based on dependencies)')// Package Filtering
+    .option('--excluded-patterns [excludedPatterns...]', 'patterns to exclude packages from processing (e.g., "**/node_modules/**", "dist/*")')// Link/Unlink Options
+    .option('--clean-node-modules', 'for unlink command: remove node_modules and package-lock.json, then reinstall dependencies')// Command-specific options (forwarded to commit/release/publish)
+    .option('--context-files [contextFiles...]', 'files containing additional context (forwarded to commit/release/publish)').option('--self-reflection', 'generate self-reflection report (forwarded to commit/release/publish)').option('--max-agentic-iterations <iterations>', 'maximum iterations for AI analysis (forwarded to commit/release/publish)', parseInt).description(`Analyze package dependencies in workspace and execute commands in dependency order.
+
+Built-in commands:
+  commit      - Run 'kodrdriv commit' in each package
+  publish     - Run 'kodrdriv publish' in each package (supports --parallel)
+  precommit   - Run precommit checks (lint -> build -> test) in each package
+  link        - Create file: dependencies for local development
+  unlink      - Restore npm registry dependencies
+  development - Switch to development branch with version bump
+  branches    - Show branch information for all packages
+  run         - Execute custom shell command (use --cmd)
+  checkout    - Checkout specified branch in all packages
+
+Command-specific options:
+  You can pass any commit, release, or publish options and they will be forwarded.
+  Examples: --context-files, --sendit, --interactive, --self-reflection
+
+  For commit options: kodrdriv commit --help
+  For release options: kodrdriv release --help
+  For publish options: kodrdriv publish --help
+
+Examples:
+  kodrdriv tree commit --context-files IMPL.md --sendit
+  kodrdriv tree publish --parallel --context-files RELEASE.md
+  kodrdriv tree publish --parallel --model "gpt-4o" --self-reflection
+  kodrdriv tree --cmd "npm test"
+  kodrdriv tree publish --continue --retry-failed
+  kodrdriv tree publish --audit-branches
+  kodrdriv tree publish --status-parallel
+  kodrdriv tree --order`);
+    addSharedOptions(treeCommand);
+    const linkCommand = program.command('link [packageArgument]').option('--scope-roots <scopeRoots>', 'JSON mapping of scopes to root directories (e.g., \'{"@company": "../"}\')').description('Create npm file: dependencies for local development');
+    addSharedOptions(linkCommand);
+    const unlinkCommand = program.command('unlink [packageArgument]').option('--scope-roots <scopeRoots>', 'JSON mapping of scopes to root directories (e.g., \'{"@company": "../"}\')').option('--clean-node-modules', 'remove node_modules and package-lock.json, then reinstall dependencies').description('Restore original dependencies and rebuild node_modules');
+    addSharedOptions(unlinkCommand);
+    const audioReviewCommand = program.command('audio-review').option('--include-commit-history', 'include recent commit log messages in context (default: true)').option('--no-include-commit-history', 'exclude commit log messages from context').option('--include-recent-diffs', 'include recent commit diffs in context (default: true)').option('--no-include-recent-diffs', 'exclude recent diffs from context').option('--include-release-notes', 'include recent release notes in context (default: false)').option('--no-include-release-notes', 'exclude release notes from context').option('--include-github-issues', 'include open GitHub issues in context (default: true)').option('--no-include-github-issues', 'exclude GitHub issues from context').option('--commit-history-limit <limit>', 'number of recent commits to include', parseInt).option('--diff-history-limit <limit>', 'number of recent commit diffs to include', parseInt).option('--release-notes-limit <limit>', 'number of recent release notes to include', parseInt).option('--github-issues-limit <limit>', 'number of open GitHub issues to include (max 20)', parseInt).option('--context <context>', 'additional context for the audio review').option('--file <file>', 'audio file path').option('--directory <directory>', 'directory containing audio files to process').option('--max-recording-time <time>', 'maximum recording time in seconds', parseInt).option('--sendit', 'Create GitHub issues automatically without confirmation').description('Record audio, transcribe with Whisper, and analyze for project issues using AI');
+    addSharedOptions(audioReviewCommand);
+    const reviewCommand = program.command('review').argument('[note]', 'review note to analyze for project issues').option('--include-commit-history', 'include recent commit log messages in context (default: true)').option('--no-include-commit-history', 'exclude commit log messages from context').option('--include-recent-diffs', 'include recent commit diffs in context (default: true)').option('--no-include-recent-diffs', 'exclude recent diffs from context').option('--include-release-notes', 'include recent release notes in context (default: false)').option('--no-include-release-notes', 'exclude release notes from context').option('--include-github-issues', 'include open GitHub issues in context (default: true)').option('--no-include-github-issues', 'exclude GitHub issues from context').option('--commit-history-limit <limit>', 'number of recent commits to include', parseInt).option('--diff-history-limit <limit>', 'number of recent commit diffs to include', parseInt).option('--release-notes-limit <limit>', 'number of recent release notes to include', parseInt).option('--github-issues-limit <limit>', 'number of open GitHub issues to include (max 20)', parseInt).option('--context <context>', 'additional context for the review').option('--file <file>', 'read review note from a file').option('--directory <directory>', 'process all review files in a directory').option('--sendit', 'Create GitHub issues automatically without confirmation').option('--editor-timeout <timeout>', 'timeout for editor in milliseconds (default: no timeout)', parseInt).description('Analyze review note for project issues using AI');
+    addSharedOptions(reviewCommand);
+    // Customize help output for review command
+    reviewCommand.configureHelp({
+        formatHelp: (cmd, helper)=>{
+            const nameAndVersion = `kodrdriv review [note] [options]\n\nAnalyze review note for project issues using AI\n`;
+            const argumentsSection = [
+                [
+                    'note',
+                    'review note to analyze for project issues (can also be piped via STDIN)'
+                ]
+            ];
+            const reviewOptions = [
+                [
+                    '--context <context>',
+                    'additional context for the review'
+                ],
+                [
+                    '--file <file>',
+                    'read review note from a file'
+                ],
+                [
+                    '--directory <directory>',
+                    'process all review files in a directory'
+                ]
+            ];
+            const gitContextOptions = [
+                [
+                    '--include-commit-history',
+                    'include recent commit log messages in context (default: true)'
+                ],
+                [
+                    '--no-include-commit-history',
+                    'exclude commit log messages from context'
+                ],
+                [
+                    '--include-recent-diffs',
+                    'include recent commit diffs in context (default: true)'
+                ],
+                [
+                    '--no-include-recent-diffs',
+                    'exclude recent diffs from context'
+                ],
+                [
+                    '--include-release-notes',
+                    'include recent release notes in context (default: false)'
+                ],
+                [
+                    '--no-include-release-notes',
+                    'exclude release notes from context'
+                ],
+                [
+                    '--include-github-issues',
+                    'include open GitHub issues in context (default: true)'
+                ],
+                [
+                    '--no-include-github-issues',
+                    'exclude GitHub issues from context'
+                ],
+                [
+                    '--commit-history-limit <limit>',
+                    'number of recent commits to include'
+                ],
+                [
+                    '--diff-history-limit <limit>',
+                    'number of recent commit diffs to include'
+                ],
+                [
+                    '--release-notes-limit <limit>',
+                    'number of recent release notes to include'
+                ],
+                [
+                    '--github-issues-limit <limit>',
+                    'number of open GitHub issues to include (max 20)'
+                ]
+            ];
+            const behavioralOptions = [
+                [
+                    '--sendit',
+                    'Create GitHub issues automatically without confirmation'
+                ]
+            ];
+            const globalOptions = [
+                [
+                    '--dry-run',
+                    'perform a dry run without saving files'
+                ],
+                [
+                    '--verbose',
+                    'enable verbose logging'
+                ],
+                [
+                    '--debug',
+                    'enable debug logging'
+                ],
+                [
+                    '--overrides',
+                    'enable overrides'
+                ],
+                [
+                    '--model <model>',
+                    'OpenAI model to use'
+                ],
+                [
+                    '--openai-reasoning <level>',
+                    'OpenAI reasoning level (low, medium, high)'
+                ],
+                [
+                    '--openai-max-output-tokens <tokens>',
+                    'OpenAI maximum output tokens'
+                ],
+                [
+                    '-d, --context-directories [contextDirectories...]',
+                    'directories to scan for context'
+                ],
+                [
+                    '--config-dir <configDir>',
+                    'configuration directory'
+                ],
+                [
+                    '--output-dir <outputDir>',
+                    'output directory for generated files'
+                ],
+                [
+                    '--excluded-paths [excludedPatterns...]',
+                    'paths to exclude from the diff'
+                ],
+                [
+                    '-h, --help',
+                    'display help for command'
+                ]
+            ];
+            const formatOptionsSection = (title, options)=>{
+                const maxWidth = Math.max(...options.map(([flag])=>flag.length));
+                return `${title}:\n` + options.map(([flag, desc])=>`  ${flag.padEnd(maxWidth + 2)} ${desc}`).join('\n') + '\n';
+            };
+            return nameAndVersion + '\n' + formatOptionsSection('Arguments', argumentsSection) + '\n' + formatOptionsSection('Options', reviewOptions) + '\n' + formatOptionsSection('Git Context Parameters', gitContextOptions) + '\n' + formatOptionsSection('Behavioral Options', behavioralOptions) + '\n' + formatOptionsSection('Global Options', globalOptions) + '\n' + 'Environment Variables:\n' + '  OPENAI_API_KEY          OpenAI API key (required)\n';
+        }
+    });
+    const cleanCommand = program.command('clean').description('Remove the output directory and all generated files');
+    addSharedOptions(cleanCommand);
+    const pullCommand = program.command('pull').option('--remote <remote>', 'remote to pull from (default: origin)', 'origin').option('--branch <branch>', 'branch to pull (default: current branch)').option('--no-auto-stash', 'do not auto-stash local changes').option('--no-auto-resolve', 'do not auto-resolve common conflicts').description('Smart pull from remote with auto-conflict resolution for common files (package-lock.json, dist/, etc.)');
+    addSharedOptions(pullCommand);
+    const precommitCommand = program.command('precommit').option('--fix', 'Attempt to auto-fix linting issues before running precommit checks').description('Run precommit checks (lint -> build -> test) with optimization');
+    addSharedOptions(precommitCommand);
+    const developmentCommand = program.command('development').option('--target-version <targetVersion>', 'target version bump type (patch, minor, major) or explicit version (e.g., "2.1.0")', 'patch').option('--no-milestones', 'disable GitHub milestone integration').option('--tag-working-branch', 'tag working branch with release version before bumping to dev (default: true)').option('--no-tag-working-branch', 'skip tagging working branch').option('--create-retroactive-tags', 'create tags for past releases found in git history (one-time operation)').option('--working-tag-prefix <prefix>', 'tag prefix for working branch tags (default: "working/")').description('Switch to working branch and set up development version');
+    addSharedOptions(developmentCommand);
+    const versionsCommand = program.command('versions <subcommand>').option('--directories [directories...]', 'directories to scan for packages (defaults to current directory)').description('Update dependency versions across packages. Subcommands: minor');
+    addSharedOptions(versionsCommand);
+    const updatesCommand = program.command('updates [scope]').option('--directories [directories...]', 'directories to scan for packages (tree mode, defaults to current directory)').option('--inter-project', 'update inter-project dependencies based on tree state (requires --scope)').option('--report', 'generate a dependency analysis report instead of updating').option('--analyze', 'run AI-powered analysis on the dependency report to get upgrade recommendations').option('--strategy <strategy>', 'strategy for analyze mode: latest, conservative, or compatible', 'latest').description('Update dependencies matching a specific scope using npm-check-updates (e.g., kodrdriv updates @fjell) or update inter-project dependencies (kodrdriv updates --inter-project @fjell)');
+    addSharedOptions(updatesCommand);
+    const selectAudioCommand = program.command('select-audio').description('Interactively select and save audio device for recording');
+    addSharedOptions(selectAudioCommand);
+    program.parse();
+    const cliArgs = program.opts(); // Get all opts initially
+    // Determine which command is being run
+    let commandName = DEFAULT_COMMAND;
+    let commandOptions = {}; // Store specific command options
+    if (program.args.length > 0) {
+        commandName = program.args[0];
+        validateCommand(commandName);
+    }
+    // Only proceed with command-specific options if validation passed
+    if (ALLOWED_COMMANDS.includes(commandName)) {
+        var _chosen_commitCommand, _chosen_commit, _chosen_audioCommitCommand, _chosen_releaseCommand, _chosen_publishCommand, _chosen_treeCommand, _chosen_linkCommand, _chosen_unlinkCommand, _chosen_audioReviewCommand, _chosen_reviewCommand, _chosen_review, _chosen_cleanCommand, _chosen_precommitCommand, _chosen_developmentCommand, _chosen_versionsCommand, _chosen_updatesCommand, _chosen_selectAudioCommand;
+        const chosen = {
+            commitCommand,
+            audioCommitCommand,
+            releaseCommand,
+            publishCommand,
+            treeCommand,
+            linkCommand,
+            unlinkCommand,
+            audioReviewCommand,
+            reviewCommand,
+            cleanCommand,
+            precommitCommand,
+            developmentCommand,
+            versionsCommand,
+            updatesCommand,
+            selectAudioCommand
+        };
+        if (commandName === 'commit' && (chosen === null || chosen === void 0 ? void 0 : (_chosen_commitCommand = chosen.commitCommand) === null || _chosen_commitCommand === void 0 ? void 0 : _chosen_commitCommand.opts)) {
+            const commitCmd = chosen.commitCommand;
+            commandOptions = commitCmd.opts();
+            // Handle positional argument for direction
+            // Try to get direction from program.args (after the command name)
+            if (program.args.length > 1) {
+                commandOptions.direction = program.args[1];
+            }
+            // Also try commitCommand.args as fallback
+            const args = commitCmd.args;
+            if (Array.isArray(args) && args.length > 0) {
+                const firstTruthyArg = args.find((arg)=>arg);
+                if (firstTruthyArg) {
+                    commandOptions.direction = firstTruthyArg;
+                }
+            }
+            // Final fallback: use locally constructed commit command's args
+            if (!commandOptions.direction) {
+                const localArgs = commitCommand === null || commitCommand === void 0 ? void 0 : commitCommand.args;
+                if (Array.isArray(localArgs) && localArgs.length > 0) {
+                    const firstLocalArg = localArgs.find((arg)=>arg);
+                    if (firstLocalArg) {
+                        commandOptions.direction = firstLocalArg;
+                    }
+                }
+            }
+            // Check for STDIN input for direction (takes precedence over positional argument)
+            const stdinInput = await readStdin();
+            if (typeof stdinInput === 'string') {
+                commandOptions.direction = stdinInput;
+            }
+        } else if (commandName === 'commit' && (chosen === null || chosen === void 0 ? void 0 : (_chosen_commit = chosen.commit) === null || _chosen_commit === void 0 ? void 0 : _chosen_commit.opts)) {
+            // Fallback when a test/mocked commands object provides 'commit' instead of 'commitCommand'
+            const commitCmd = chosen.commit;
+            commandOptions = commitCmd.opts();
+            if (program.args.length > 1) {
+                commandOptions.direction = program.args[1];
+            }
+            const args = commitCmd.args;
+            if (Array.isArray(args) && args.length > 0) {
+                const firstTruthyArg = args.find((arg)=>arg);
+                if (firstTruthyArg) {
+                    commandOptions.direction = firstTruthyArg;
+                }
+            }
+            if (!commandOptions.direction) {
+                const localArgs = commitCommand === null || commitCommand === void 0 ? void 0 : commitCommand.args;
+                if (Array.isArray(localArgs) && localArgs.length > 0) {
+                    const firstLocalArg = localArgs.find((arg)=>arg);
+                    if (firstLocalArg) {
+                        commandOptions.direction = firstLocalArg;
+                    }
+                }
+            }
+            const stdinInput = await readStdin();
+            if (typeof stdinInput === 'string') {
+                commandOptions.direction = stdinInput;
+            }
+        } else if (commandName === 'audio-commit' && (chosen === null || chosen === void 0 ? void 0 : (_chosen_audioCommitCommand = chosen.audioCommitCommand) === null || _chosen_audioCommitCommand === void 0 ? void 0 : _chosen_audioCommitCommand.opts)) {
+            const audioCommitCmd = chosen.audioCommitCommand;
+            commandOptions = audioCommitCmd.opts();
+        } else if (commandName === 'release' && (chosen === null || chosen === void 0 ? void 0 : (_chosen_releaseCommand = chosen.releaseCommand) === null || _chosen_releaseCommand === void 0 ? void 0 : _chosen_releaseCommand.opts)) {
+            const releaseCmd = chosen.releaseCommand;
+            commandOptions = releaseCmd.opts();
+        } else if (commandName === 'publish' && (chosen === null || chosen === void 0 ? void 0 : (_chosen_publishCommand = chosen.publishCommand) === null || _chosen_publishCommand === void 0 ? void 0 : _chosen_publishCommand.opts)) {
+            const publishCmd = chosen.publishCommand;
+            commandOptions = publishCmd.opts();
+        } else if (commandName === 'tree' && (chosen === null || chosen === void 0 ? void 0 : (_chosen_treeCommand = chosen.treeCommand) === null || _chosen_treeCommand === void 0 ? void 0 : _chosen_treeCommand.opts)) {
+            const treeCmd = chosen.treeCommand;
+            commandOptions = treeCmd.opts();
+            // Handle positional arguments for built-in command and package argument
+            const args = treeCmd.args;
+            if (Array.isArray(args) && args.length > 0) {
+                const firstTruthyArg = args.find((arg)=>arg);
+                if (firstTruthyArg) {
+                    commandOptions.builtInCommand = firstTruthyArg;
+                    if ((firstTruthyArg === 'link' || firstTruthyArg === 'unlink' || firstTruthyArg === 'run' || firstTruthyArg === 'checkout' || firstTruthyArg === 'updates') && args.length > 1) {
+                        const secondTruthyArg = args.slice(1).find((arg)=>arg);
+                        if (secondTruthyArg) {
+                            commandOptions.packageArgument = secondTruthyArg;
+                        }
+                    }
+                }
+            }
+            const stdinInput = await readStdin();
+            if (typeof stdinInput === 'string') {
+                commandOptions.builtInCommand = stdinInput.trim().split('\n')[0] || commandOptions.builtInCommand;
+                const stdinLines = stdinInput.split('\n');
+                if (stdinLines[1]) {
+                    commandOptions.packageArgument = stdinLines[1];
+                }
+            }
+        } else if (commandName === 'link' && (chosen === null || chosen === void 0 ? void 0 : (_chosen_linkCommand = chosen.linkCommand) === null || _chosen_linkCommand === void 0 ? void 0 : _chosen_linkCommand.opts)) {
+            const linkCmd = chosen.linkCommand;
+            commandOptions = linkCmd.opts();
+            const args = linkCmd.args;
+            if (Array.isArray(args) && args.length > 0) {
+                const firstTruthyArg = args.find((arg)=>arg);
+                if (firstTruthyArg) {
+                    commandOptions.packageArgument = firstTruthyArg === 'status' ? 'status' : firstTruthyArg;
+                }
+            }
+            const stdinInput = await readStdin();
+            if (typeof stdinInput === 'string') {
+                commandOptions.packageArgument = stdinInput;
+            }
+        } else if (commandName === 'unlink' && (chosen === null || chosen === void 0 ? void 0 : (_chosen_unlinkCommand = chosen.unlinkCommand) === null || _chosen_unlinkCommand === void 0 ? void 0 : _chosen_unlinkCommand.opts)) {
+            const unlinkCmd = chosen.unlinkCommand;
+            commandOptions = unlinkCmd.opts();
+            const args = unlinkCmd.args;
+            if (Array.isArray(args) && args.length > 0) {
+                const firstTruthyArg = args.find((arg)=>arg);
+                if (firstTruthyArg) {
+                    commandOptions.packageArgument = firstTruthyArg === 'status' ? 'status' : firstTruthyArg;
+                }
+            }
+            const stdinInput = await readStdin();
+            if (typeof stdinInput === 'string') {
+                commandOptions.packageArgument = stdinInput;
+            }
+        } else if (commandName === 'audio-review' && (chosen === null || chosen === void 0 ? void 0 : (_chosen_audioReviewCommand = chosen.audioReviewCommand) === null || _chosen_audioReviewCommand === void 0 ? void 0 : _chosen_audioReviewCommand.opts)) {
+            const audioReviewCmd = chosen.audioReviewCommand;
+            commandOptions = audioReviewCmd.opts();
+        } else if (commandName === 'review' && (chosen === null || chosen === void 0 ? void 0 : (_chosen_reviewCommand = chosen.reviewCommand) === null || _chosen_reviewCommand === void 0 ? void 0 : _chosen_reviewCommand.opts)) {
+            const reviewCmd = chosen.reviewCommand;
+            commandOptions = reviewCmd.opts();
+            const args = reviewCmd.args;
+            if (Array.isArray(args) && args.length > 0) {
+                const firstTruthyArg = args.find((arg)=>arg);
+                if (firstTruthyArg) {
+                    commandOptions.note = firstTruthyArg;
+                }
+            }
+            // Final fallback: use locally constructed review command's args
+            if (!commandOptions.note) {
+                const localArgs = reviewCommand === null || reviewCommand === void 0 ? void 0 : reviewCommand.args;
+                if (Array.isArray(localArgs) && localArgs.length > 0) {
+                    const firstLocalArg = localArgs.find((arg)=>arg);
+                    if (firstLocalArg) {
+                        commandOptions.note = firstLocalArg;
+                    }
+                }
+            }
+            const stdinInput = await readStdin();
+            if (typeof stdinInput === 'string') {
+                commandOptions.note = stdinInput;
+            }
+        } else if (commandName === 'review' && (chosen === null || chosen === void 0 ? void 0 : (_chosen_review = chosen.review) === null || _chosen_review === void 0 ? void 0 : _chosen_review.opts)) {
+            const reviewCmd = chosen.review;
+            commandOptions = reviewCmd.opts();
+            const args = reviewCmd.args;
+            if (Array.isArray(args) && args.length > 0) {
+                const firstTruthyArg = args.find((arg)=>arg);
+                if (firstTruthyArg) {
+                    commandOptions.note = firstTruthyArg;
+                }
+            }
+            const stdinInput = await readStdin();
+            if (typeof stdinInput === 'string') {
+                commandOptions.note = stdinInput;
+            }
+        } else if (commandName === 'clean' && (chosen === null || chosen === void 0 ? void 0 : (_chosen_cleanCommand = chosen.cleanCommand) === null || _chosen_cleanCommand === void 0 ? void 0 : _chosen_cleanCommand.opts)) {
+            const cleanCmd = chosen.cleanCommand;
+            commandOptions = cleanCmd.opts();
+        } else if (commandName === 'precommit' && (chosen === null || chosen === void 0 ? void 0 : (_chosen_precommitCommand = chosen.precommitCommand) === null || _chosen_precommitCommand === void 0 ? void 0 : _chosen_precommitCommand.opts)) {
+            const precommitCmd = chosen.precommitCommand;
+            commandOptions = precommitCmd.opts();
+        } else if (commandName === 'development' && (chosen === null || chosen === void 0 ? void 0 : (_chosen_developmentCommand = chosen.developmentCommand) === null || _chosen_developmentCommand === void 0 ? void 0 : _chosen_developmentCommand.opts)) {
+            const developmentCmd = chosen.developmentCommand;
+            commandOptions = developmentCmd.opts();
+        } else if (commandName === 'versions' && (chosen === null || chosen === void 0 ? void 0 : (_chosen_versionsCommand = chosen.versionsCommand) === null || _chosen_versionsCommand === void 0 ? void 0 : _chosen_versionsCommand.opts)) {
+            const versionsCmd = chosen.versionsCommand;
+            commandOptions = versionsCmd.opts();
+            const args = versionsCmd.args;
+            if (args && args.length > 0 && args[0]) {
+                commandOptions.subcommand = args[0];
+            }
+        } else if (commandName === 'updates' && (chosen === null || chosen === void 0 ? void 0 : (_chosen_updatesCommand = chosen.updatesCommand) === null || _chosen_updatesCommand === void 0 ? void 0 : _chosen_updatesCommand.opts)) {
+            const updatesCmd = chosen.updatesCommand;
+            commandOptions = updatesCmd.opts();
+            const args = updatesCmd.args;
+            if (args && args.length > 0 && args[0]) {
+                commandOptions.scope = args[0];
+            }
+        } else if (commandName === 'select-audio' && (chosen === null || chosen === void 0 ? void 0 : (_chosen_selectAudioCommand = chosen.selectAudioCommand) === null || _chosen_selectAudioCommand === void 0 ? void 0 : _chosen_selectAudioCommand.opts)) {
+            const selectAudioCmd = chosen.selectAudioCommand;
+            commandOptions = selectAudioCmd.opts();
+        } else {
+            // Final fallback
+            commandOptions = program.opts();
+        }
+    }
+    // Include command name in CLI args for merging
+    const finalCliArgs = {
+        ...cliArgs,
+        ...commandOptions
+    };
+    // Final safety fallback for positional arguments when STDIN is null and mocks provide args on constructed commands
+    if (commandName === 'commit' && !finalCliArgs.direction) {
+        const localArgs = commitCommand === null || commitCommand === void 0 ? void 0 : commitCommand.args;
+        if (Array.isArray(localArgs) && localArgs.length > 0) {
+            const firstLocalArg = localArgs.find((arg)=>arg);
+            if (firstLocalArg) {
+                finalCliArgs.direction = firstLocalArg;
+            }
+        }
+    }
+    if (commandName === 'review' && !finalCliArgs.note) {
+        const localArgs = reviewCommand === null || reviewCommand === void 0 ? void 0 : reviewCommand.args;
+        if (Array.isArray(localArgs) && localArgs.length > 0) {
+            const firstLocalArg = localArgs.find((arg)=>arg);
+            if (firstLocalArg) {
+                finalCliArgs.note = firstLocalArg;
+            }
+        }
+    }
+    const commandConfig = {
+        commandName
+    };
+    return [
+        finalCliArgs,
+        commandConfig
+    ];
+}
+async function validateAndProcessSecureOptions() {
+    // For check-config and init-config commands, we don't want to throw an error for missing API key
+    const isCheckConfig = process.argv.includes('--check-config');
+    const isInitConfig = process.argv.includes('--init-config');
+    if (!process.env.OPENAI_API_KEY && !isCheckConfig && !isInitConfig) {
+        throw new Error('OpenAI API key is required. Please set the OPENAI_API_KEY environment variable.');
+    }
+    // Prefer CLI key if provided, otherwise use env var (might be undefined for check-config/init-config)
+    const openaiApiKey = process.env.OPENAI_API_KEY;
+    const secureConfig = {
+        openaiApiKey: openaiApiKey
+    };
+    return secureConfig;
+}
+// Renamed validation function to reflect its broader role
+async function validateAndProcessOptions(options) {
+    var _options_dryRun, _options_verbose, _options_debug, _options_overrides, _options_model, _options_openaiReasoning, _options_openaiMaxOutputTokens, _options_outputDirectory, _options_preferencesDirectory, _options_discoveredConfigDirs, _options_resolvedConfigDirs, _options_excludedPatterns, _options_branches;
+    const contextDirectories = await validateContextDirectories(options.contextDirectories || KODRDRIV_DEFAULTS.contextDirectories);
+    const configDir = options.configDirectory || KODRDRIV_DEFAULTS.configDirectory;
+    // Skip config directory validation since Cardigantime handles hierarchical lookup
+    // Ensure all required fields are present and have correct types after merging
+    const finalConfig = {
+        dryRun: (_options_dryRun = options.dryRun) !== null && _options_dryRun !== void 0 ? _options_dryRun : KODRDRIV_DEFAULTS.dryRun,
+        verbose: (_options_verbose = options.verbose) !== null && _options_verbose !== void 0 ? _options_verbose : KODRDRIV_DEFAULTS.verbose,
+        debug: (_options_debug = options.debug) !== null && _options_debug !== void 0 ? _options_debug : KODRDRIV_DEFAULTS.debug,
+        overrides: (_options_overrides = options.overrides) !== null && _options_overrides !== void 0 ? _options_overrides : KODRDRIV_DEFAULTS.overrides,
+        model: (_options_model = options.model) !== null && _options_model !== void 0 ? _options_model : KODRDRIV_DEFAULTS.model,
+        openaiReasoning: (_options_openaiReasoning = options.openaiReasoning) !== null && _options_openaiReasoning !== void 0 ? _options_openaiReasoning : KODRDRIV_DEFAULTS.openaiReasoning,
+        openaiMaxOutputTokens: (_options_openaiMaxOutputTokens = options.openaiMaxOutputTokens) !== null && _options_openaiMaxOutputTokens !== void 0 ? _options_openaiMaxOutputTokens : KODRDRIV_DEFAULTS.openaiMaxOutputTokens,
+        contextDirectories: contextDirectories,
+        configDirectory: configDir,
+        outputDirectory: (_options_outputDirectory = options.outputDirectory) !== null && _options_outputDirectory !== void 0 ? _options_outputDirectory : KODRDRIV_DEFAULTS.outputDirectory,
+        preferencesDirectory: (_options_preferencesDirectory = options.preferencesDirectory) !== null && _options_preferencesDirectory !== void 0 ? _options_preferencesDirectory : KODRDRIV_DEFAULTS.preferencesDirectory,
+        // Cardigantime-specific properties (from fileValues or defaults)
+        discoveredConfigDirs: (_options_discoveredConfigDirs = options.discoveredConfigDirs) !== null && _options_discoveredConfigDirs !== void 0 ? _options_discoveredConfigDirs : [],
+        resolvedConfigDirs: (_options_resolvedConfigDirs = options.resolvedConfigDirs) !== null && _options_resolvedConfigDirs !== void 0 ? _options_resolvedConfigDirs : [],
+        // Command-specific options - ensure all defaults are present even for partial configs
+        commit: {
+            ...KODRDRIV_DEFAULTS.commit,
+            ...Object.fromEntries(Object.entries(options.commit || {}).filter(([_, v])=>v !== undefined && v !== null))
+        },
+        audioCommit: {
+            ...KODRDRIV_DEFAULTS.audioCommit,
+            ...Object.fromEntries(Object.entries(options.audioCommit || {}).filter(([_, v])=>v !== undefined))
+        },
+        release: {
+            ...KODRDRIV_DEFAULTS.release,
+            ...Object.fromEntries(Object.entries(options.release || {}).filter(([_, v])=>v !== undefined))
+        },
+        audioReview: {
+            ...KODRDRIV_DEFAULTS.audioReview,
+            ...Object.fromEntries(Object.entries(options.audioReview || {}).filter(([_, v])=>v !== undefined))
+        },
+        review: {
+            ...KODRDRIV_DEFAULTS.review,
+            ...Object.fromEntries(Object.entries(options.review || {}).filter(([_, v])=>v !== undefined))
+        },
+        publish: {
+            ...KODRDRIV_DEFAULTS.publish,
+            ...Object.fromEntries(Object.entries(options.publish || {}).filter(([_, v])=>v !== undefined))
+        },
+        link: {
+            ...KODRDRIV_DEFAULTS.link,
+            ...Object.fromEntries(Object.entries(options.link || {}).filter(([_, v])=>v !== undefined))
+        },
+        unlink: {
+            ...KODRDRIV_DEFAULTS.unlink,
+            ...Object.fromEntries(Object.entries(options.unlink || {}).filter(([_, v])=>v !== undefined))
+        },
+        tree: {
+            ...KODRDRIV_DEFAULTS.tree,
+            ...Object.fromEntries(Object.entries(options.tree || {}).filter(([_, v])=>v !== undefined))
+        },
+        development: {
+            ...KODRDRIV_DEFAULTS.development,
+            ...Object.fromEntries(Object.entries(options.development || {}).filter(([_, v])=>v !== undefined))
+        },
+        versions: {
+            ...KODRDRIV_DEFAULTS.versions,
+            ...Object.fromEntries(Object.entries(options.versions || {}).filter(([_, v])=>v !== undefined))
+        },
+        updates: {
+            ...KODRDRIV_DEFAULTS.updates,
+            ...Object.fromEntries(Object.entries(options.updates || {}).filter(([_, v])=>v !== undefined))
+        },
+        excludedPatterns: (_options_excludedPatterns = options.excludedPatterns) !== null && _options_excludedPatterns !== void 0 ? _options_excludedPatterns : KODRDRIV_DEFAULTS.excludedPatterns,
+        branches: (_options_branches = options.branches) !== null && _options_branches !== void 0 ? _options_branches : KODRDRIV_DEFAULTS.branches
+    };
+    // Final validation against the MainConfig shape (optional, cardigantime might handle it)
+    // You could potentially use ConfigShape.parse(finalConfig) here if needed
+    return finalConfig;
+}
+// Export for testing
+function validateCommand(commandName) {
+    if (!ALLOWED_COMMANDS.includes(commandName)) {
+        throw new Error(`Invalid command: ${commandName}, allowed commands: ${ALLOWED_COMMANDS.join(', ')}`);
+    }
+    return commandName;
+}
+// Export for testing
+async function validateContextDirectories(contextDirectories) {
+    const logger = getLogger();
+    const storage = createStorage();
+    // Filter out directories that don't exist
+    const validDirectories = [];
+    for (const dir of contextDirectories){
+        try {
+            if (await storage.isDirectoryReadable(dir)) {
+                validDirectories.push(dir);
+            } else {
+                logger.warn(`DIRECTORY_NOT_READABLE: Directory not readable | Directory: ${dir} | Impact: Cannot scan for packages`);
+            }
+        } catch (error) {
+            logger.warn(`DIRECTORY_VALIDATION_ERROR: Error validating directory | Directory: ${dir} | Error: ${error.message}`);
+        }
+    }
+    return validDirectories;
+}
+
+export { configure, getCliConfig, transformCliArgs, validateAndProcessOptions, validateAndProcessSecureOptions, validateCommand, validateContextDirectories };
+//# sourceMappingURL=arguments.js.map