skiller 0.4.3

package/dist/core/config-utils.js

@@ -0,0 +1,30 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.mapRawAgentConfigs = mapRawAgentConfigs;
+/**
+ * Maps raw agent configuration keys to their corresponding agent identifiers.
+ *
+ * This function normalizes configuration keys by matching them against agent identifiers
+ * and display names. It performs both exact matching (case-insensitive) with agent
+ * identifiers and substring matching (case-insensitive) with agent display names
+ * for backwards compatibility.
+ *
+ * @param raw Raw agent configurations with user-provided keys
+ * @param agents Array of all available agents
+ * @returns Record with agent identifiers as keys and their configurations as values
+ */
+function mapRawAgentConfigs(raw, agents) {
+    const mappedConfigs = {};
+    for (const [key, cfg] of Object.entries(raw)) {
+        const lowerKey = key.toLowerCase();
+        for (const agent of agents) {
+            const identifier = agent.getIdentifier();
+            // Exact match with identifier or substring match with display name for backwards compatibility
+            if (identifier === lowerKey ||
+                agent.getName().toLowerCase().includes(lowerKey)) {
+                mappedConfigs[identifier] = cfg;
+            }
+        }
+    }
+    return mappedConfigs;
+}

package/dist/core/hash.js

@@ -0,0 +1,24 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.sha256 = sha256;
+exports.stableJson = stableJson;
+const crypto_1 = require("crypto");
+function sha256(data) {
+    return (0, crypto_1.createHash)('sha256').update(data, 'utf8').digest('hex');
+}
+// Stable JSON stringify: sorts object keys recursively.
+function stableJson(value) {
+    return JSON.stringify(sortValue(value));
+}
+function sortValue(value) {
+    if (Array.isArray(value)) {
+        return value.map(sortValue);
+    }
+    if (value && typeof value === 'object') {
+        const entries = Object.entries(value)
+            .sort(([a], [b]) => (a < b ? -1 : a > b ? 1 : 0))
+            .map(([k, v]) => [k, sortValue(v)]);
+        return Object.fromEntries(entries);
+    }
+    return value;
+}

package/dist/core/revert-engine.js

@@ -0,0 +1,413 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.revertAgentConfiguration = revertAgentConfiguration;
+exports.cleanUpAuxiliaryFiles = cleanUpAuxiliaryFiles;
+const path = __importStar(require("path"));
+const fs_1 = require("fs");
+const agent_utils_1 = require("../agents/agent-utils");
+const mcp_1 = require("../paths/mcp");
+const constants_1 = require("../constants");
+const settings_1 = require("../vscode/settings");
+/**
+ * Checks if a file exists.
+ */
+async function fileExists(filePath) {
+    try {
+        await fs_1.promises.access(filePath);
+        return true;
+    }
+    catch {
+        return false;
+    }
+}
+/**
+ * Restores a file from its backup if the backup exists.
+ */
+async function restoreFromBackup(filePath, verbose, dryRun) {
+    const backupPath = `${filePath}.bak`;
+    const backupExists = await fileExists(backupPath);
+    if (!backupExists) {
+        (0, constants_1.logVerbose)(`No backup found for: ${filePath}`, verbose);
+        return false;
+    }
+    const prefix = (0, constants_1.actionPrefix)(dryRun);
+    if (dryRun) {
+        (0, constants_1.logVerbose)(`${prefix} Would restore: ${filePath} from backup`, verbose);
+    }
+    else {
+        await fs_1.promises.copyFile(backupPath, filePath);
+        (0, constants_1.logVerbose)(`${prefix} Restored: ${filePath} from backup`, verbose);
+    }
+    return true;
+}
+/**
+ * Removes a file if it exists and has no backup (meaning it was generated by ruler).
+ */
+async function removeGeneratedFile(filePath, verbose, dryRun) {
+    const fileExistsFlag = await fileExists(filePath);
+    const backupExists = await fileExists(`${filePath}.bak`);
+    if (!fileExistsFlag) {
+        (0, constants_1.logVerbose)(`File does not exist: ${filePath}`, verbose);
+        return false;
+    }
+    if (backupExists) {
+        (0, constants_1.logVerbose)(`File has backup, skipping removal: ${filePath}`, verbose);
+        return false;
+    }
+    const prefix = (0, constants_1.actionPrefix)(dryRun);
+    if (dryRun) {
+        (0, constants_1.logVerbose)(`${prefix} Would remove generated file: ${filePath}`, verbose);
+    }
+    else {
+        await fs_1.promises.unlink(filePath);
+        (0, constants_1.logVerbose)(`${prefix} Removed generated file: ${filePath}`, verbose);
+    }
+    return true;
+}
+/**
+ * Removes backup files.
+ */
+async function removeBackupFile(filePath, verbose, dryRun) {
+    const backupPath = `${filePath}.bak`;
+    const backupExists = await fileExists(backupPath);
+    if (!backupExists) {
+        return false;
+    }
+    const prefix = (0, constants_1.actionPrefix)(dryRun);
+    if (dryRun) {
+        (0, constants_1.logVerbose)(`${prefix} Would remove backup file: ${backupPath}`, verbose);
+    }
+    else {
+        await fs_1.promises.unlink(backupPath);
+        (0, constants_1.logVerbose)(`${prefix} Removed backup file: ${backupPath}`, verbose);
+    }
+    return true;
+}
+/**
+ * Recursively checks if a directory contains only empty directories
+ */
+async function isDirectoryTreeEmpty(dirPath) {
+    try {
+        const entries = await fs_1.promises.readdir(dirPath);
+        if (entries.length === 0) {
+            return true;
+        }
+        for (const entry of entries) {
+            const entryPath = path.join(dirPath, entry);
+            const entryStat = await fs_1.promises.stat(entryPath);
+            if (entryStat.isFile()) {
+                return false;
+            }
+            else if (entryStat.isDirectory()) {
+                const isEmpty = await isDirectoryTreeEmpty(entryPath);
+                if (!isEmpty) {
+                    return false;
+                }
+            }
+        }
+        return true;
+    }
+    catch {
+        return false;
+    }
+}
+/**
+ * Helper function to execute directory removal with consistent dry-run handling and logging.
+ */
+async function executeDirectoryAction(dirPath, action, verbose, dryRun) {
+    const prefix = (0, constants_1.actionPrefix)(dryRun);
+    const actionText = action === 'remove-tree' ? 'directory tree' : 'directory';
+    if (dryRun) {
+        (0, constants_1.logVerbose)(`${prefix} Would remove empty ${actionText}: ${dirPath}`, verbose);
+    }
+    else {
+        await fs_1.promises.rm(dirPath, { recursive: true });
+        (0, constants_1.logVerbose)(`${prefix} Removed empty ${actionText}: ${dirPath}`, verbose);
+    }
+    return true;
+}
+/**
+ * Attempts to remove a single empty directory if it exists and is empty.
+ */
+async function removeEmptyDirectory(dirPath, verbose, dryRun, logMissing = false) {
+    try {
+        const stat = await fs_1.promises.stat(dirPath);
+        if (!stat.isDirectory()) {
+            return false;
+        }
+        const isEmpty = await isDirectoryTreeEmpty(dirPath);
+        if (isEmpty) {
+            return await executeDirectoryAction(dirPath, 'remove-tree', verbose, dryRun);
+        }
+        return false;
+    }
+    catch {
+        if (logMissing) {
+            (0, constants_1.logVerbose)(`Directory ${dirPath} doesn't exist or can't be accessed`, verbose);
+        }
+        return false;
+    }
+}
+/**
+ * Handles special cleanup logic for .augment directory and its rules subdirectory.
+ */
+async function removeAugmentDirectory(projectRoot, verbose, dryRun) {
+    const augmentDir = path.join(projectRoot, '.augment');
+    let directoriesRemoved = 0;
+    try {
+        const augmentStat = await fs_1.promises.stat(augmentDir);
+        if (!augmentStat.isDirectory()) {
+            return 0;
+        }
+        const rulesDir = path.join(augmentDir, 'rules');
+        const rulesRemoved = await removeEmptyDirectory(rulesDir, verbose, dryRun);
+        if (rulesRemoved) {
+            directoriesRemoved++;
+        }
+        const augmentRemoved = await removeEmptyDirectory(augmentDir, verbose, dryRun);
+        if (augmentRemoved) {
+            directoriesRemoved++;
+        }
+    }
+    catch {
+        // .augment directory doesn't exist, that's fine. leaving comment as catch block can't be kept empty.
+    }
+    return directoriesRemoved;
+}
+/**
+ * Removes empty directories that were created by ruler.
+ * Only removes directories if they are empty and were likely created by ruler.
+ * Special handling for .augment directory to clean up rules subdirectory.
+ */
+async function removeEmptyDirectories(projectRoot, verbose, dryRun) {
+    const rulerCreatedDirs = [
+        '.github',
+        '.cursor',
+        '.windsurf',
+        '.junie',
+        '.openhands',
+        '.idx',
+        '.gemini',
+        '.vscode',
+        '.augmentcode',
+        '.kilocode',
+    ];
+    let directoriesRemoved = 0;
+    // Handle .augment directory with special logic
+    directoriesRemoved += await removeAugmentDirectory(projectRoot, verbose, dryRun);
+    // Handle all other ruler-created directories
+    for (const dirName of rulerCreatedDirs) {
+        const dirPath = path.join(projectRoot, dirName);
+        const removed = await removeEmptyDirectory(dirPath, verbose, dryRun, true);
+        if (removed) {
+            directoriesRemoved++;
+        }
+    }
+    return directoriesRemoved;
+}
+/**
+ * Removes additional files created by specific agents that aren't covered by their main output paths.
+ */
+async function removeAdditionalAgentFiles(projectRoot, verbose, dryRun) {
+    const additionalFiles = [
+        '.gemini/settings.json',
+        '.mcp.json',
+        '.vscode/mcp.json',
+        '.cursor/mcp.json',
+        '.kilocode/mcp.json',
+        'config.toml',
+    ];
+    let filesRemoved = 0;
+    const prefix = (0, constants_1.actionPrefix)(dryRun);
+    for (const filePath of additionalFiles) {
+        const fullPath = path.join(projectRoot, filePath);
+        try {
+            const fileExistsFlag = await fileExists(fullPath);
+            if (!fileExistsFlag) {
+                continue;
+            }
+            const backupExists = await fileExists(`${fullPath}.bak`);
+            if (backupExists) {
+                const restored = await restoreFromBackup(fullPath, verbose, dryRun);
+                if (restored) {
+                    filesRemoved++;
+                }
+            }
+            else {
+                if (dryRun) {
+                    (0, constants_1.logVerbose)(`${prefix} Would remove additional file: ${fullPath}`, verbose);
+                }
+                else {
+                    await fs_1.promises.unlink(fullPath);
+                    (0, constants_1.logVerbose)(`${prefix} Removed additional file: ${fullPath}`, verbose);
+                }
+                filesRemoved++;
+            }
+        }
+        catch {
+            (0, constants_1.logVerbose)(`Additional file ${fullPath} doesn't exist or can't be accessed`, verbose);
+        }
+    }
+    const settingsPath = (0, settings_1.getVSCodeSettingsPath)(projectRoot);
+    const backupPath = `${settingsPath}.bak`;
+    if (await fileExists(backupPath)) {
+        const restored = await restoreFromBackup(settingsPath, verbose, dryRun);
+        if (restored) {
+            filesRemoved++;
+            (0, constants_1.logVerbose)(`${constants_1.actionPrefix} Restored VSCode settings from backup`, verbose);
+        }
+    }
+    else if (await fileExists(settingsPath)) {
+        try {
+            if (dryRun) {
+                const settings = await (0, settings_1.readVSCodeSettings)(settingsPath);
+                if (settings['augment.advanced']) {
+                    delete settings['augment.advanced'];
+                    const remainingKeys = Object.keys(settings);
+                    if (remainingKeys.length === 0) {
+                        (0, constants_1.logVerbose)(`${constants_1.actionPrefix} Would remove empty VSCode settings file`, verbose);
+                    }
+                    else {
+                        (0, constants_1.logVerbose)(`${constants_1.actionPrefix} Would remove augment.advanced section from ${settingsPath}`, verbose);
+                    }
+                    filesRemoved++;
+                }
+            }
+            else {
+                const settings = await (0, settings_1.readVSCodeSettings)(settingsPath);
+                if (settings['augment.advanced']) {
+                    delete settings['augment.advanced'];
+                    const remainingKeys = Object.keys(settings);
+                    if (remainingKeys.length === 0) {
+                        await fs_1.promises.unlink(settingsPath);
+                        (0, constants_1.logVerbose)(`${constants_1.actionPrefix} Removed empty VSCode settings file`, verbose);
+                    }
+                    else {
+                        await (0, settings_1.writeVSCodeSettings)(settingsPath, settings);
+                        (0, constants_1.logVerbose)(`${constants_1.actionPrefix} Removed augment.advanced section from VSCode settings`, verbose);
+                    }
+                    filesRemoved++;
+                }
+                else {
+                    (0, constants_1.logVerbose)(`No augment.advanced section found in ${settingsPath}`, verbose);
+                }
+            }
+        }
+        catch (error) {
+            (0, constants_1.logVerbose)(`Failed to process VSCode settings.json: ${error}`, verbose);
+        }
+    }
+    return filesRemoved;
+}
+/**
+ * Reverts configuration for a single agent.
+ * @param agent The agent to revert
+ * @param projectRoot Root directory of the project
+ * @param agentConfig Agent-specific configuration
+ * @param keepBackups Whether to keep backup files
+ * @param verbose Whether to enable verbose logging
+ * @param dryRun Whether to perform a dry run
+ * @returns Promise resolving to revert statistics
+ */
+async function revertAgentConfiguration(agent, projectRoot, agentConfig, keepBackups, verbose, dryRun) {
+    const result = {
+        restored: 0,
+        removed: 0,
+        backupsRemoved: 0,
+    };
+    const outputPaths = (0, agent_utils_1.getAgentOutputPaths)(agent, projectRoot, agentConfig);
+    (0, constants_1.logVerbose)(`Agent ${agent.getName()} output paths: ${outputPaths.join(', ')}`, verbose);
+    for (const outputPath of outputPaths) {
+        const restored = await restoreFromBackup(outputPath, verbose, dryRun);
+        if (restored) {
+            result.restored++;
+            if (!keepBackups) {
+                const backupRemoved = await removeBackupFile(outputPath, verbose, dryRun);
+                if (backupRemoved) {
+                    result.backupsRemoved++;
+                }
+            }
+        }
+        else {
+            const removed = await removeGeneratedFile(outputPath, verbose, dryRun);
+            if (removed) {
+                result.removed++;
+            }
+        }
+    }
+    // Handle MCP files
+    const mcpPath = await (0, mcp_1.getNativeMcpPath)(agent.getName(), projectRoot);
+    if (mcpPath && mcpPath.startsWith(projectRoot)) {
+        if (agent.getName() === 'AugmentCode' &&
+            mcpPath.endsWith('.vscode/settings.json')) {
+            (0, constants_1.logVerbose)(`Skipping MCP handling for AugmentCode settings.json - handled separately`, verbose);
+        }
+        else {
+            const mcpRestored = await restoreFromBackup(mcpPath, verbose, dryRun);
+            if (mcpRestored) {
+                result.restored++;
+                if (!keepBackups) {
+                    const mcpBackupRemoved = await removeBackupFile(mcpPath, verbose, dryRun);
+                    if (mcpBackupRemoved) {
+                        result.backupsRemoved++;
+                    }
+                }
+            }
+            else {
+                const mcpRemoved = await removeGeneratedFile(mcpPath, verbose, dryRun);
+                if (mcpRemoved) {
+                    result.removed++;
+                }
+            }
+        }
+    }
+    return result;
+}
+/**
+ * Cleans up auxiliary files and directories.
+ * @param projectRoot Root directory of the project
+ * @param verbose Whether to enable verbose logging
+ * @param dryRun Whether to perform a dry run
+ * @returns Promise resolving to cleanup statistics
+ */
+async function cleanUpAuxiliaryFiles(projectRoot, verbose, dryRun) {
+    const additionalFilesRemoved = await removeAdditionalAgentFiles(projectRoot, verbose, dryRun);
+    const directoriesRemoved = await removeEmptyDirectories(projectRoot, verbose, dryRun);
+    return {
+        additionalFilesRemoved,
+        directoriesRemoved,
+    };
+}

package/dist/lib.js

@@ -0,0 +1,196 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.allAgents = void 0;
+exports.applyAllAgentConfigs = applyAllAgentConfigs;
+const path = __importStar(require("path"));
+const agents_1 = require("./agents");
+Object.defineProperty(exports, "allAgents", { enumerable: true, get: function () { return agents_1.allAgents; } });
+const constants_1 = require("./constants");
+const apply_engine_1 = require("./core/apply-engine");
+const config_utils_1 = require("./core/config-utils");
+const agent_selection_1 = require("./core/agent-selection");
+const agents = agents_1.allAgents;
+/**
+ * Resolves skills enabled state based on precedence: CLI flag > ruler.toml > default (enabled)
+ */
+function resolveSkillsEnabled(cliFlag, configSetting) {
+    return cliFlag !== undefined
+        ? cliFlag
+        : configSetting !== undefined
+            ? configSetting
+            : true; // default to enabled
+}
+/**
+ * Resolves backup setting from CLI flag, config file, or default.
+ * Precedence: CLI > Config > Default (true)
+ */
+function resolveBackupEnabled(cliFlag, configSetting) {
+    return cliFlag !== undefined
+        ? cliFlag
+        : configSetting !== undefined
+            ? configSetting
+            : true; // default to enabled
+}
+/**
+ * Applies ruler configurations for all supported AI agents.
+ * @param projectRoot Root directory of the project
+ */
+/**
+ * Applies ruler configurations for selected AI agents.
+ * @param projectRoot Root directory of the project
+ * @param includedAgents Optional list of agent name filters (case-insensitive substrings)
+ */
+async function applyAllAgentConfigs(projectRoot, includedAgents, configPath, cliMcpEnabled = true, cliMcpStrategy, cliGitignoreEnabled, verbose = false, dryRun = false, localOnly = false, nested = false, cliBackupEnabled, skillsEnabled) {
+    // Load configuration and rules
+    (0, constants_1.logVerbose)(`Loading configuration from project root: ${projectRoot}`, verbose);
+    if (configPath) {
+        (0, constants_1.logVerbose)(`Using custom config path: ${configPath}`, verbose);
+    }
+    let selectedAgents;
+    let generatedPaths;
+    let loadedConfig;
+    if (nested) {
+        const hierarchicalConfigs = await (0, apply_engine_1.loadNestedConfigurations)(projectRoot, configPath, localOnly, nested);
+        if (hierarchicalConfigs.length === 0) {
+            throw new Error('No .ruler directories found');
+        }
+        (0, constants_1.logWarn)('Nested mode is experimental and may change in future releases.', dryRun);
+        // Use the root config for agent selection (all levels share the same agent settings)
+        const rootConfigEntry = selectRootConfiguration(hierarchicalConfigs, projectRoot);
+        const rootConfig = rootConfigEntry.config;
+        loadedConfig = rootConfig;
+        rootConfig.cliAgents = includedAgents;
+        (0, constants_1.logVerbose)(`Loaded ${hierarchicalConfigs.length} .ruler directory configurations`, verbose);
+        (0, constants_1.logVerbose)(`Root configuration has ${Object.keys(rootConfig.agentConfigs).length} agent configs`, verbose);
+        for (const configEntry of hierarchicalConfigs) {
+            normalizeAgentConfigs(configEntry.config, agents);
+        }
+        selectedAgents = (0, agent_selection_1.resolveSelectedAgents)(rootConfig, agents);
+        (0, constants_1.logVerbose)(`Selected ${selectedAgents.length} agents: ${selectedAgents.map((a) => a.getName()).join(', ')}`, verbose);
+        // Propagate skills if enabled - do this for each nested directory
+        const skillsEnabledResolved = resolveSkillsEnabled(skillsEnabled, rootConfig.skills?.enabled);
+        if (skillsEnabledResolved) {
+            const { propagateSkills, generateSkillsFromRules } = await Promise.resolve().then(() => __importStar(require('./core/SkillsProcessor')));
+            // Generate skills from .mdc files if enabled
+            const generateFromRules = rootConfig.skills?.generate_from_rules ?? false;
+            if (generateFromRules) {
+                for (const configEntry of hierarchicalConfigs) {
+                    const nestedRoot = path.dirname(configEntry.rulerDir);
+                    (0, constants_1.logVerbose)(`Generating skills from .mdc files for nested directory: ${nestedRoot}`, verbose);
+                    await generateSkillsFromRules(nestedRoot, configEntry.rulerDir, verbose, dryRun);
+                }
+            }
+            // Propagate skills for each nested .ruler directory
+            for (const configEntry of hierarchicalConfigs) {
+                const nestedRoot = path.dirname(configEntry.rulerDir);
+                (0, constants_1.logVerbose)(`Propagating skills for nested directory: ${nestedRoot}`, verbose);
+                await propagateSkills(nestedRoot, selectedAgents, skillsEnabledResolved, verbose, dryRun, configEntry.rulerDir);
+            }
+        }
+        // Resolve backup setting: CLI > Config > Default (true)
+        const backupResolved = resolveBackupEnabled(cliBackupEnabled, rootConfig.backup?.enabled);
+        generatedPaths = await (0, apply_engine_1.processHierarchicalConfigurations)(selectedAgents, hierarchicalConfigs, verbose, dryRun, cliMcpEnabled, cliMcpStrategy, backupResolved, skillsEnabledResolved);
+    }
+    else {
+        const singleConfig = await (0, apply_engine_1.loadSingleConfiguration)(projectRoot, configPath, localOnly);
+        loadedConfig = singleConfig.config;
+        singleConfig.config.cliAgents = includedAgents;
+        (0, constants_1.logVerbose)(`Loaded configuration with ${Object.keys(singleConfig.config.agentConfigs).length} agent configs`, verbose);
+        (0, constants_1.logVerbose)(`Found .ruler directory with ${singleConfig.concatenatedRules.length} characters of rules`, verbose);
+        normalizeAgentConfigs(singleConfig.config, agents);
+        selectedAgents = (0, agent_selection_1.resolveSelectedAgents)(singleConfig.config, agents);
+        (0, constants_1.logVerbose)(`Selected ${selectedAgents.length} agents: ${selectedAgents.map((a) => a.getName()).join(', ')}`, verbose);
+        // Propagate skills if enabled
+        const skillsEnabledResolved = resolveSkillsEnabled(skillsEnabled, singleConfig.config.skills?.enabled);
+        if (skillsEnabledResolved) {
+            const { propagateSkills, generateSkillsFromRules } = await Promise.resolve().then(() => __importStar(require('./core/SkillsProcessor')));
+            // Generate skills from .mdc files if enabled
+            const generateFromRules = singleConfig.config.skills?.generate_from_rules ?? false;
+            if (generateFromRules) {
+                (0, constants_1.logVerbose)('Generating skills from .mdc files', verbose);
+                await generateSkillsFromRules(projectRoot, singleConfig.rulerDir, verbose, dryRun);
+            }
+            await propagateSkills(projectRoot, selectedAgents, skillsEnabledResolved, verbose, dryRun, singleConfig.rulerDir);
+        }
+        // Resolve backup setting: CLI > Config > Default (true)
+        const backupResolved = resolveBackupEnabled(cliBackupEnabled, singleConfig.config.backup?.enabled);
+        generatedPaths = await (0, apply_engine_1.processSingleConfiguration)(selectedAgents, singleConfig, projectRoot, verbose, dryRun, cliMcpEnabled, cliMcpStrategy, backupResolved, skillsEnabledResolved);
+    }
+    // Add skills-generated paths to gitignore if skills are enabled
+    let allGeneratedPaths = generatedPaths;
+    const skillsEnabledForGitignore = resolveSkillsEnabled(skillsEnabled, loadedConfig.skills?.enabled);
+    if (skillsEnabledForGitignore) {
+        // Skills enabled by default or explicitly
+        const { getSkillsGitignorePaths } = await Promise.resolve().then(() => __importStar(require('./core/SkillsProcessor')));
+        const skillsPaths = await getSkillsGitignorePaths(projectRoot);
+        allGeneratedPaths = [...generatedPaths, ...skillsPaths];
+    }
+    await (0, apply_engine_1.updateGitignore)(projectRoot, allGeneratedPaths, loadedConfig, cliGitignoreEnabled, dryRun);
+}
+/**
+ * Normalizes per-agent config keys to agent identifiers for consistent lookup.
+ * Maps both exact identifier matches and substring matches with agent names.
+ * @param config The configuration object to normalize
+ * @param agents Array of available agents
+ */
+function normalizeAgentConfigs(config, agents) {
+    // Normalize per-agent config keys to agent identifiers (exact match or substring match)
+    config.agentConfigs = (0, config_utils_1.mapRawAgentConfigs)(config.agentConfigs, agents);
+}
+function selectRootConfiguration(configurations, projectRoot) {
+    if (configurations.length === 0) {
+        throw new Error('No hierarchical configurations available');
+    }
+    const normalizedProjectRoot = path.resolve(projectRoot);
+    let bestIndex = -1;
+    let bestDepth = Number.POSITIVE_INFINITY;
+    for (let i = 0; i < configurations.length; i++) {
+        const entry = configurations[i];
+        const normalizedDir = path.resolve(entry.rulerDir);
+        if (!normalizedDir.startsWith(normalizedProjectRoot)) {
+            continue;
+        }
+        const depth = normalizedDir.split(path.sep).length;
+        if (depth < bestDepth) {
+            bestDepth = depth;
+            bestIndex = i;
+        }
+    }
+    if (bestIndex === -1) {
+        return configurations[0];
+    }
+    return configurations[bestIndex];
+}