wave-agent-sdk 0.9.1 → 0.9.3

package/dist/core/session.d.ts

@@ -1,3 +1,3 @@
-export { listSessions, truncateContent, loadSessionFromJsonl, } from "../services/session.js";
+export { listSessions, truncateContent, loadSessionFromJsonl, loadFullMessageThread, } from "../services/session.js";
 export type { SessionMetadata, SessionData } from "../services/session.js";
 //# sourceMappingURL=session.d.ts.map

package/dist/core/session.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"session.d.ts","sourceRoot":"","sources":["../../src/core/session.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,YAAY,EACZ,eAAe,EACf,oBAAoB,GACrB,MAAM,wBAAwB,CAAC;AAChC,YAAY,EAAE,eAAe,EAAE,WAAW,EAAE,MAAM,wBAAwB,CAAC"}
+{"version":3,"file":"session.d.ts","sourceRoot":"","sources":["../../src/core/session.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,YAAY,EACZ,eAAe,EACf,oBAAoB,EACpB,qBAAqB,GACtB,MAAM,wBAAwB,CAAC;AAChC,YAAY,EAAE,eAAe,EAAE,WAAW,EAAE,MAAM,wBAAwB,CAAC"}

package/dist/core/session.js

@@ -1 +1 @@
-export { listSessions, truncateContent, loadSessionFromJsonl, } from "../services/session.js";
+export { listSessions, truncateContent, loadSessionFromJsonl, loadFullMessageThread, } from "../services/session.js";

package/dist/managers/liveConfigManager.d.ts

@@ -29,7 +29,7 @@ export declare class LiveConfigManager {
     /**
      * Initialize configuration watching
      * Maps to FR-004: System MUST watch settings.json files
-     * Supports watching multiple file paths (e.g., settings.local.json and settings.json)
+     * Supports watching multiple file paths (e.g., local settings.local.json and settings.json)
      */
     private initializeWatching;
     /**
@@ -74,10 +74,6 @@ export declare class LiveConfigManager {
     };
     private setupFileWatcherEvents;
     private handleFileChange;
-    /**
-     * Validate configuration structure and content
-     */
-    private validateConfiguration;
     private detectChanges;
     /**
      * Get configuration file paths for user and project settings

package/dist/managers/liveConfigManager.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"liveConfigManager.d.ts","sourceRoot":"","sources":["../../src/managers/liveConfigManager.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAmBH,OAAO,EAAE,SAAS,EAAE,MAAM,uBAAuB,CAAC;AAElD,OAAO,KAAK,EAEV,iBAAiB,EAClB,MAAM,2BAA2B,CAAC;AAInC,MAAM,WAAW,wBAAwB;IACvC,OAAO,EAAE,MAAM,CAAC;CACjB;AAED,qBAAa,iBAAiB;IAgB1B,OAAO,CAAC,SAAS;IAfnB,OAAO,CAAC,QAAQ,CAAC,OAAO,CAAS;IACjC,OAAO,CAAC,aAAa,CAAkB;IAGvC,OAAO,CAAC,oBAAoB,CAAkC;IAC9D,OAAO,CAAC,sBAAsB,CAAkC;IAGhE,OAAO,CAAC,WAAW,CAAqB;IACxC,OAAO,CAAC,eAAe,CAAC,CAAW;IACnC,OAAO,CAAC,kBAAkB,CAAC,CAAW;IACtC,OAAO,CAAC,UAAU,CAAkB;IACpC,OAAO,CAAC,gBAAgB,CAAkB;gBAGhC,SAAS,EAAE,SAAS,EAC5B,OAAO,EAAE,wBAAwB;IAOnC,OAAO,KAAK,WAAW,GAEtB;IAED,OAAO,KAAK,iBAAiB,GAE5B;IAED,OAAO,KAAK,oBAAoB,GAE/B;IAED;;;;OAIG;YACW,kBAAkB;IA0ChC;;OAEG;IACH,uBAAuB,IAAI,iBAAiB,GAAG,IAAI;IAInD;;OAEG;IACG,UAAU,IAAI,OAAO,CAAC,IAAI,CAAC;IAmBjC;;OAEG;IACG,QAAQ,IAAI,OAAO,CAAC,IAAI,CAAC;IAsB/B;;;OAGG;YACW,mBAAmB;IAmLjC;;OAEG;IACG,MAAM,IAAI,OAAO,CAAC,iBAAiB,CAAC;IAI1C;;OAEG;IACH,gBAAgB,IAAI,OAAO;IAI3B;;OAEG;IACH,gBAAgB;;;;;;;;;;;;IAgBhB,OAAO,CAAC,sBAAsB;YAMhB,gBAAgB;IAmC9B;;OAEG;IACH,OAAO,CAAC,qBAAqB;IA4F7B,OAAO,CAAC,aAAa;IAuDrB;;;OAGG;IACH,OAAO,CAAC,qBAAqB;CAQ9B"}
+{"version":3,"file":"liveConfigManager.d.ts","sourceRoot":"","sources":["../../src/managers/liveConfigManager.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAaH,OAAO,EAAE,SAAS,EAAE,MAAM,uBAAuB,CAAC;AAElD,OAAO,KAAK,EAEV,iBAAiB,EAClB,MAAM,2BAA2B,CAAC;AAInC,MAAM,WAAW,wBAAwB;IACvC,OAAO,EAAE,MAAM,CAAC;CACjB;AAED,qBAAa,iBAAiB;IAgB1B,OAAO,CAAC,SAAS;IAfnB,OAAO,CAAC,QAAQ,CAAC,OAAO,CAAS;IACjC,OAAO,CAAC,aAAa,CAAkB;IAGvC,OAAO,CAAC,oBAAoB,CAAkC;IAC9D,OAAO,CAAC,sBAAsB,CAAkC;IAGhE,OAAO,CAAC,WAAW,CAAqB;IACxC,OAAO,CAAC,eAAe,CAAC,CAAW;IACnC,OAAO,CAAC,kBAAkB,CAAC,CAAW;IACtC,OAAO,CAAC,UAAU,CAAkB;IACpC,OAAO,CAAC,gBAAgB,CAAkB;gBAGhC,SAAS,EAAE,SAAS,EAC5B,OAAO,EAAE,wBAAwB;IAOnC,OAAO,KAAK,WAAW,GAEtB;IAED,OAAO,KAAK,iBAAiB,GAE5B;IAED,OAAO,KAAK,oBAAoB,GAE/B;IAED;;;;OAIG;YACW,kBAAkB;IA0ChC;;OAEG;IACH,uBAAuB,IAAI,iBAAiB,GAAG,IAAI;IAInD;;OAEG;IACG,UAAU,IAAI,OAAO,CAAC,IAAI,CAAC;IAmBjC;;OAEG;IACG,QAAQ,IAAI,OAAO,CAAC,IAAI,CAAC;IAsB/B;;;OAGG;YACW,mBAAmB;IAuIjC;;OAEG;IACG,MAAM,IAAI,OAAO,CAAC,iBAAiB,CAAC;IAI1C;;OAEG;IACH,gBAAgB,IAAI,OAAO;IAI3B;;OAEG;IACH,gBAAgB;;;;;;;;;;;;IAgBhB,OAAO,CAAC,sBAAsB;YAMhB,gBAAgB;IAmC9B,OAAO,CAAC,aAAa;IAuDrB;;;OAGG;IACH,OAAO,CAAC,qBAAqB;CAU9B"}

package/dist/managers/liveConfigManager.js

@@ -8,8 +8,7 @@
  */
 import { existsSync } from "fs";
 import { FileWatcherService, } from "../services/fileWatcher.js";
-import { getProjectConfigPaths, getUserConfigPaths, } from "../utils/configPaths.js";
-import { isValidHookEvent, isValidHookEventConfig } from "../types/hooks.js";
+import { isValidHookEvent } from "../types/hooks.js";
 import { ensureGlobalGitIgnore } from "../utils/fileUtils.js";
 import { logger } from "../utils/globalLogger.js";
 export class LiveConfigManager {
@@ -37,7 +36,7 @@ export class LiveConfigManager {
     /**
      * Initialize configuration watching
      * Maps to FR-004: System MUST watch settings.json files
-     * Supports watching multiple file paths (e.g., settings.local.json and settings.json)
+     * Supports watching multiple file paths (e.g., local settings.local.json and settings.json)
      */
     async initializeWatching(userPaths, projectPaths) {
         try {
@@ -51,7 +50,7 @@ export class LiveConfigManager {
                     await this.fileWatcher.watchFile(userPath, (event) => this.handleFileChange(event, "user"));
                 }
             }
-            // Start watching project configs that exist
+            // Start watching local configs that exist
             if (projectPaths) {
                 for (const projectPath of projectPaths) {
                     if (existsSync(projectPath)) {
@@ -160,32 +159,6 @@ export class LiveConfigManager {
             if (loadResult.warnings && loadResult.warnings.length > 0) {
                 logger?.warn(`Live Config: Configuration warnings: ${loadResult.warnings.join("; ")}`);
             }
-            // Validate new configuration if it exists
-            if (newConfig) {
-                const validation = this.validateConfiguration(newConfig);
-                if (!validation.valid) {
-                    const errorMessage = `Configuration validation failed: ${validation.errors.join(", ")}`;
-                    logger?.error(`Live Config: ${errorMessage}`);
-                    // Use previous valid configuration for error recovery
-                    if (this.lastValidConfiguration) {
-                        this.currentConfiguration = this.lastValidConfiguration;
-                        // Apply environment variables to configuration service if configured
-                        if (this.lastValidConfiguration.env) {
-                            this.configurationService.setEnvironmentVars(this.lastValidConfiguration.env);
-                        }
-                        // Update hook manager if available
-                        if (this.hookManager) {
-                            this.hookManager.loadConfigurationFromWaveConfig(this.lastValidConfiguration);
-                        }
-                        return this.currentConfiguration;
-                    }
-                    else {
-                        logger?.warn("Live Config: No previous valid configuration available, using empty config");
-                        this.currentConfiguration = {};
-                        return this.currentConfiguration;
-                    }
-                }
-            }
             // Detect changes between old and new configuration
             this.detectChanges(this.currentConfiguration, newConfig);
             // Update current configuration
@@ -202,18 +175,10 @@ export class LiveConfigManager {
             }
             // Update permission manager if available
             if (this.permissionManager) {
-                if (this.currentConfiguration.permissions?.defaultMode) {
-                    this.permissionManager.updateConfiguredDefaultMode(this.currentConfiguration.permissions.defaultMode);
-                }
-                if (this.currentConfiguration.permissions?.allow) {
-                    this.permissionManager.updateAllowedRules(this.currentConfiguration.permissions.allow);
-                }
-                if (this.currentConfiguration.permissions?.deny) {
-                    this.permissionManager.updateDeniedRules(this.currentConfiguration.permissions.deny);
-                }
-                if (this.currentConfiguration.permissions?.additionalDirectories) {
-                    this.permissionManager.updateAdditionalDirectories(this.currentConfiguration.permissions.additionalDirectories);
-                }
+                this.permissionManager.updateConfiguredDefaultMode(this.currentConfiguration.permissions?.defaultMode);
+                this.permissionManager.updateAllowedRules(this.currentConfiguration.permissions?.allow || []);
+                this.permissionManager.updateDeniedRules(this.currentConfiguration.permissions?.deny || []);
+                this.permissionManager.updateAdditionalDirectories(this.currentConfiguration.permissions?.additionalDirectories || []);
             }
             return this.currentConfiguration;
         }
@@ -302,87 +267,6 @@ export class LiveConfigManager {
             logger?.error(`Live Config: Error handling file change for ${source} config: ${error.message}`);
         }
     }
-    /**
-     * Validate configuration structure and content
-     */
-    validateConfiguration(config) {
-        const errors = [];
-        if (!config || typeof config !== "object") {
-            return { valid: false, errors: ["Configuration must be an object"] };
-        }
-        // Validate permissions if present
-        if (config.permissions) {
-            if (typeof config.permissions !== "object") {
-                errors.push("permissions property must be an object");
-            }
-            else {
-                // Validate defaultMode if present
-                if (config.permissions.defaultMode !== undefined) {
-                    const validModes = [
-                        "default",
-                        "bypassPermissions",
-                        "acceptEdits",
-                        "plan",
-                    ];
-                    if (!validModes.includes(config.permissions.defaultMode)) {
-                        errors.push(`Invalid defaultMode: "${config.permissions.defaultMode}". Must be one of: ${validModes.join(", ")}`);
-                    }
-                }
-                // Validate allow if present
-                if (config.permissions.allow) {
-                    if (!Array.isArray(config.permissions.allow)) {
-                        errors.push("permissions.allow must be an array");
-                    }
-                }
-            }
-        }
-        // Validate hooks if present
-        if (config.hooks) {
-            if (typeof config.hooks !== "object") {
-                errors.push("hooks property must be an object");
-            }
-            else {
-                // Validate each hook event
-                for (const [eventName, eventConfigs] of Object.entries(config.hooks)) {
-                    // Validate event name
-                    if (!isValidHookEvent(eventName)) {
-                        errors.push(`Invalid hook event: ${eventName}`);
-                        continue;
-                    }
-                    // Validate event configurations
-                    if (!Array.isArray(eventConfigs)) {
-                        errors.push(`Hook event ${eventName} must be an array of configurations`);
-                        continue;
-                    }
-                    eventConfigs.forEach((eventConfig, index) => {
-                        if (!isValidHookEventConfig(eventConfig)) {
-                            errors.push(`Invalid hook event configuration at ${eventName}[${index}]`);
-                        }
-                    });
-                }
-            }
-        }
-        // Validate environment variables if present
-        if (config.env) {
-            if (typeof config.env !== "object" || Array.isArray(config.env)) {
-                errors.push("env property must be an object");
-            }
-            else {
-                for (const [key, value] of Object.entries(config.env)) {
-                    if (typeof key !== "string" || key.trim() === "") {
-                        errors.push(`Invalid environment variable key: ${key}`);
-                    }
-                    if (typeof value !== "string") {
-                        errors.push(`Environment variable ${key} must have a string value`);
-                    }
-                }
-            }
-        }
-        return {
-            valid: errors.length === 0,
-            errors,
-        };
-    }
     detectChanges(oldConfig, newConfig) {
         const added = [];
         const modified = [];
@@ -428,8 +312,10 @@ export class LiveConfigManager {
      * Returns paths in priority order (local.json first, then .json)
      */
     getConfigurationPaths() {
-        const userPaths = getUserConfigPaths();
-        const projectPaths = getProjectConfigPaths(this.workdir);
-        return { userPaths, projectPaths };
+        const paths = this.configurationService.getConfigurationPaths(this.workdir);
+        return {
+            userPaths: paths.userPaths,
+            projectPaths: paths.projectPaths,
+        };
     }
 }

package/dist/managers/permissionManager.d.ts

@@ -31,6 +31,7 @@ export declare class PermissionManager {
     private deniedRules;
     private temporaryRules;
     private additionalDirectories;
+    private systemAdditionalDirectories;
     private workdir?;
     private planFilePath?;
     private onConfiguredDefaultModeChange?;
@@ -84,6 +85,10 @@ export declare class PermissionManager {
      * Update the additional directories (e.g., when configuration reloads)
      */
     updateAdditionalDirectories(directories: string[]): void;
+    /**
+     * Add a system-level additional directory that is persistent across configuration reloads
+     */
+    addSystemAdditionalDirectory(directory: string): void;
     /**
      * Update the working directory
      */

package/dist/managers/permissionManager.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"permissionManager.d.ts","sourceRoot":"","sources":["../../src/managers/permissionManager.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAIH,OAAO,KAAK,EACV,kBAAkB,EAClB,qBAAqB,EACrB,kBAAkB,EAClB,cAAc,EACf,MAAM,yBAAyB,CAAC;AAEjC,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,mBAAmB,CAAC;AAgBhD,OAAO,EAAE,SAAS,EAAE,MAAM,uBAAuB,CAAC;AA8BlD,MAAM,WAAW,wBAAwB;IACvC,uDAAuD;IACvD,qBAAqB,CAAC,EAAE,cAAc,CAAC;IACvC,kCAAkC;IAClC,YAAY,CAAC,EAAE,MAAM,EAAE,CAAC;IACxB,iCAAiC;IACjC,WAAW,CAAC,EAAE,MAAM,EAAE,CAAC;IACvB,8DAA8D;IAC9D,qBAAqB,CAAC,EAAE,MAAM,EAAE,CAAC;IACjC,iCAAiC;IACjC,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,oCAAoC;IACpC,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,sBAAsB;IACtB,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB;AAED,qBAAa,iBAAiB;IAY1B,OAAO,CAAC,SAAS;IAXnB,OAAO,CAAC,qBAAqB,CAAC,CAAiB;IAC/C,OAAO,CAAC,YAAY,CAAgB;IACpC,OAAO,CAAC,WAAW,CAAgB;IACnC,OAAO,CAAC,cAAc,CAAgB;IACtC,OAAO,CAAC,qBAAqB,CAAgB;IAC7C,OAAO,CAAC,OAAO,CAAC,CAAS;IACzB,OAAO,CAAC,YAAY,CAAC,CAAS;IAC9B,OAAO,CAAC,6BAA6B,CAAC,CAAiC;IACvE,OAAO,CAAC,OAAO,CAAC,CAAS;gBAGf,SAAS,EAAE,SAAS,EAC5B,OAAO,GAAE,wBAA6B;IAWxC;;OAEG;IACI,gCAAgC,CACrC,QAAQ,EAAE,CAAC,IAAI,EAAE,cAAc,KAAK,IAAI,GACvC,IAAI;IAIP;;OAEG;IACH,2BAA2B,CAAC,WAAW,CAAC,EAAE,cAAc,GAAG,IAAI;IAc/D;;OAEG;IACI,wBAAwB,IAAI,cAAc,GAAG,SAAS;IAI7D;;OAEG;IACI,eAAe,IAAI,MAAM,EAAE;IAIlC;;OAEG;IACI,cAAc,IAAI,MAAM,EAAE;IAIjC;;OAEG;IACI,wBAAwB,IAAI,MAAM,EAAE;IAI3C;;OAEG;IACI,sBAAsB,IAAI,MAAM,EAAE;IAIzC;;OAEG;IACH,kBAAkB,CAAC,KAAK,EAAE,MAAM,EAAE,GAAG,IAAI;IAIzC;;OAEG;IACH,iBAAiB,CAAC,KAAK,EAAE,MAAM,EAAE,GAAG,IAAI;IAIxC;;OAEG;IACI,iBAAiB,CAAC,KAAK,EAAE,MAAM,EAAE,GAAG,IAAI;IAI/C;;OAEG;IACI,mBAAmB,IAAI,IAAI;IAIlC;;OAEG;IACH,2BAA2B,CAAC,WAAW,EAAE,MAAM,EAAE,GAAG,IAAI;IASxD;;OAEG;IACH,aAAa,CAAC,OAAO,EAAE,MAAM,GAAG,IAAI;IAIpC;;OAEG;IACI,eAAe,CAAC,IAAI,EAAE,MAAM,GAAG,SAAS,GAAG,IAAI;IAItD;;OAEG;IACI,eAAe,IAAI,MAAM,GAAG,SAAS;IAI5C;;OAEG;IACH,OAAO,CAAC,gBAAgB;IA2BxB;;OAEG;IACH,uBAAuB,CAAC,iBAAiB,CAAC,EAAE,cAAc,GAAG,cAAc;IAI3E;;OAEG;IACH,8BAA8B,CAC5B,iBAAiB,CAAC,EAAE,cAAc,GACjC,cAAc;IAejB;;;OAGG;IACG,eAAe,CACnB,OAAO,EAAE,qBAAqB,GAC7B,OAAO,CAAC,kBAAkB,CAAC;IAyH9B;;OAEG;IACH,gBAAgB,CAAC,QAAQ,EAAE,MAAM,GAAG,OAAO;IAI3C;;OAEG;IACH,aAAa,CACX,QAAQ,EAAE,MAAM,EAChB,cAAc,EAAE,cAAc,EAC9B,QAAQ,CAAC,EAAE,kBAAkB,EAC7B,SAAS,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAClC,qBAAqB;IAgFxB;;OAEG;IACH,OAAO,CAAC,WAAW;IAwDnB;;OAEG;IACH,OAAO,CAAC,eAAe;IAiGvB;;;;;;;OAOG;IACI,cAAc,CAAC,OAAO,EAAE,MAAM,EAAE,OAAO,EAAE,MAAM,GAAG,MAAM,EAAE;IAmFjE;;;OAGG;IACU,iBAAiB,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC;CA4C5D"}
+{"version":3,"file":"permissionManager.d.ts","sourceRoot":"","sources":["../../src/managers/permissionManager.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAIH,OAAO,KAAK,EACV,kBAAkB,EAClB,qBAAqB,EACrB,kBAAkB,EAClB,cAAc,EACf,MAAM,yBAAyB,CAAC;AAEjC,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,mBAAmB,CAAC;AAgBhD,OAAO,EAAE,SAAS,EAAE,MAAM,uBAAuB,CAAC;AA8BlD,MAAM,WAAW,wBAAwB;IACvC,uDAAuD;IACvD,qBAAqB,CAAC,EAAE,cAAc,CAAC;IACvC,kCAAkC;IAClC,YAAY,CAAC,EAAE,MAAM,EAAE,CAAC;IACxB,iCAAiC;IACjC,WAAW,CAAC,EAAE,MAAM,EAAE,CAAC;IACvB,8DAA8D;IAC9D,qBAAqB,CAAC,EAAE,MAAM,EAAE,CAAC;IACjC,iCAAiC;IACjC,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,oCAAoC;IACpC,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,sBAAsB;IACtB,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB;AAED,qBAAa,iBAAiB;IAa1B,OAAO,CAAC,SAAS;IAZnB,OAAO,CAAC,qBAAqB,CAAC,CAAiB;IAC/C,OAAO,CAAC,YAAY,CAAgB;IACpC,OAAO,CAAC,WAAW,CAAgB;IACnC,OAAO,CAAC,cAAc,CAAgB;IACtC,OAAO,CAAC,qBAAqB,CAAgB;IAC7C,OAAO,CAAC,2BAA2B,CAAgB;IACnD,OAAO,CAAC,OAAO,CAAC,CAAS;IACzB,OAAO,CAAC,YAAY,CAAC,CAAS;IAC9B,OAAO,CAAC,6BAA6B,CAAC,CAAiC;IACvE,OAAO,CAAC,OAAO,CAAC,CAAS;gBAGf,SAAS,EAAE,SAAS,EAC5B,OAAO,GAAE,wBAA6B;IAWxC;;OAEG;IACI,gCAAgC,CACrC,QAAQ,EAAE,CAAC,IAAI,EAAE,cAAc,KAAK,IAAI,GACvC,IAAI;IAIP;;OAEG;IACH,2BAA2B,CAAC,WAAW,CAAC,EAAE,cAAc,GAAG,IAAI;IAc/D;;OAEG;IACI,wBAAwB,IAAI,cAAc,GAAG,SAAS;IAI7D;;OAEG;IACI,eAAe,IAAI,MAAM,EAAE;IAIlC;;OAEG;IACI,cAAc,IAAI,MAAM,EAAE;IAIjC;;OAEG;IACI,wBAAwB,IAAI,MAAM,EAAE;IAI3C;;OAEG;IACI,sBAAsB,IAAI,MAAM,EAAE;IAIzC;;OAEG;IACH,kBAAkB,CAAC,KAAK,EAAE,MAAM,EAAE,GAAG,IAAI;IAIzC;;OAEG;IACH,iBAAiB,CAAC,KAAK,EAAE,MAAM,EAAE,GAAG,IAAI;IAIxC;;OAEG;IACI,iBAAiB,CAAC,KAAK,EAAE,MAAM,EAAE,GAAG,IAAI;IAI/C;;OAEG;IACI,mBAAmB,IAAI,IAAI;IAIlC;;OAEG;IACH,2BAA2B,CAAC,WAAW,EAAE,MAAM,EAAE,GAAG,IAAI;IASxD;;OAEG;IACI,4BAA4B,CAAC,SAAS,EAAE,MAAM,GAAG,IAAI;IAW5D;;OAEG;IACH,aAAa,CAAC,OAAO,EAAE,MAAM,GAAG,IAAI;IAIpC;;OAEG;IACI,eAAe,CAAC,IAAI,EAAE,MAAM,GAAG,SAAS,GAAG,IAAI;IAItD;;OAEG;IACI,eAAe,IAAI,MAAM,GAAG,SAAS;IAI5C;;OAEG;IACH,OAAO,CAAC,gBAAgB;IAkCxB;;OAEG;IACH,uBAAuB,CAAC,iBAAiB,CAAC,EAAE,cAAc,GAAG,cAAc;IAI3E;;OAEG;IACH,8BAA8B,CAC5B,iBAAiB,CAAC,EAAE,cAAc,GACjC,cAAc;IAejB;;;OAGG;IACG,eAAe,CACnB,OAAO,EAAE,qBAAqB,GAC7B,OAAO,CAAC,kBAAkB,CAAC;IAyH9B;;OAEG;IACH,gBAAgB,CAAC,QAAQ,EAAE,MAAM,GAAG,OAAO;IAI3C;;OAEG;IACH,aAAa,CACX,QAAQ,EAAE,MAAM,EAChB,cAAc,EAAE,cAAc,EAC9B,QAAQ,CAAC,EAAE,kBAAkB,EAC7B,SAAS,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAClC,qBAAqB;IAgFxB;;OAEG;IACH,OAAO,CAAC,WAAW;IA0EnB;;OAEG;IACH,OAAO,CAAC,eAAe;IAiGvB;;;;;;;OAOG;IACI,cAAc,CAAC,OAAO,EAAE,MAAM,EAAE,OAAO,EAAE,MAAM,GAAG,MAAM,EAAE;IAmFjE;;;OAGG;IACU,iBAAiB,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC;CA4C5D"}

package/dist/managers/permissionManager.js

@@ -42,6 +42,7 @@ export class PermissionManager {
         this.deniedRules = [];
         this.temporaryRules = [];
         this.additionalDirectories = [];
+        this.systemAdditionalDirectories = [];
         this.configuredDefaultMode = options.configuredDefaultMode;
         this.allowedRules = options.allowedRules || [];
         this.deniedRules = options.deniedRules || [];
@@ -133,6 +134,17 @@ export class PermissionManager {
             return path.resolve(dir);
         });
     }
+    /**
+     * Add a system-level additional directory that is persistent across configuration reloads
+     */
+    addSystemAdditionalDirectory(directory) {
+        const resolvedPath = this.workdir && !path.isAbsolute(directory)
+            ? path.resolve(this.workdir, directory)
+            : path.resolve(directory);
+        if (!this.systemAdditionalDirectories.includes(resolvedPath)) {
+            this.systemAdditionalDirectories.push(resolvedPath);
+        }
+    }
     /**
      * Update the working directory
      */
@@ -170,6 +182,12 @@ export class PermissionManager {
                 return { isInside: true, resolvedPath: absolutePath };
             }
         }
+        // Check system additional directories
+        for (const dir of this.systemAdditionalDirectories) {
+            if (isPathInside(absolutePath, dir)) {
+                return { isInside: true, resolvedPath: absolutePath };
+            }
+        }
         return { isInside: false, resolvedPath: absolutePath };
     }
     /**
@@ -418,7 +436,20 @@ export class PermissionManager {
             const targetPath = (context.toolInput?.file_path ||
                 context.toolInput?.path);
             if (targetPath) {
-                return minimatch(targetPath, pattern, { dot: true });
+                if (minimatch(targetPath, pattern, { dot: true })) {
+                    return true;
+                }
+                // If direct match fails, try matching relative path if targetPath is absolute and pattern is relative
+                if (path.isAbsolute(targetPath) &&
+                    !path.isAbsolute(pattern) &&
+                    this.workdir) {
+                    const relativePath = path.relative(this.workdir, targetPath);
+                    // Ensure the path is not outside the workdir (doesn't start with ..)
+                    if (!relativePath.startsWith("..") &&
+                        !path.isAbsolute(relativePath)) {
+                        return minimatch(relativePath, pattern, { dot: true });
+                    }
+                }
             }
         }
         return false;

package/dist/services/configurationService.d.ts

@@ -34,10 +34,6 @@ export declare class ConfigurationService {
      * Validate configuration file without loading
      */
     validateConfigurationFile(filePath: string): ValidationResult;
-    /**
-     * Get currently loaded configuration
-     */
-    getCurrentConfiguration(): WaveConfiguration | null;
     /**
      * Set environment variables from configuration
      * This replaces direct process.env modification
@@ -101,7 +97,7 @@ export declare class ConfigurationService {
      */
     getConfigurationPaths(workdir: string): ConfigurationPaths;
     /**
-     * Add a permission rule to the project's settings.local.json
+     * Add a permission rule to the local settings.local.json
      */
     addAllowedRule(workdir: string, rule: string): Promise<void>;
     /**
@@ -135,21 +131,6 @@ export declare function mergeEnvironmentConfig(userEnv: Record<string, string> |
  * Supports both hooks and environment variables with proper validation
  */
 export declare function loadWaveConfigFromFile(filePath: string): WaveConfiguration | null;
-/**
- * Load Wave configuration from multiple file paths in priority order
- * Returns the first valid configuration found, or null if none exist
- */
-export declare function loadWaveConfigFromFiles(filePaths: string[]): WaveConfiguration | null;
-/**
- * Load user-specific Wave configuration
- * Checks .local.json first, then falls back to .json
- */
-export declare function loadUserWaveConfig(): WaveConfiguration | null;
-/**
- * Load project-specific Wave configuration
- * Checks .local.json first, then falls back to .json
- */
-export declare function loadProjectWaveConfig(workdir: string): WaveConfiguration | null;
 /**
  * Load and merge Wave configuration from both user and project sources
  * Project configuration takes precedence over user configuration

package/dist/services/configurationService.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"configurationService.d.ts","sourceRoot":"","sources":["../../src/services/configurationService.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAKH,OAAO,KAAK,EACV,uBAAuB,EACvB,gBAAgB,EAChB,kBAAkB,EAClB,iBAAiB,EACjB,KAAK,EACN,MAAM,2BAA2B,CAAC;AAOnC,OAAO,EACL,KAAK,2BAA2B,EAChC,KAAK,wBAAwB,EAC7B,KAAK,uBAAuB,EAE7B,MAAM,yBAAyB,CAAC;AACjC,OAAO,EACL,aAAa,EACb,WAAW,EAGX,cAAc,EACd,YAAY,EACb,MAAM,mBAAmB,CAAC;AAK3B,OAAO,EAAE,aAAa,EAAE,MAAM,QAAQ,CAAC;AAGvC;;;;;GAKG;AACH,qBAAa,oBAAoB;IAC/B,OAAO,CAAC,oBAAoB,CAAkC;IAC9D,OAAO,CAAC,GAAG,CAA8B;IACzC,OAAO,CAAC,OAAO,CAAoB;IAEnC;;OAEG;IACH,UAAU,CAAC,OAAO,EAAE,YAAY,GAAG,IAAI;IAMvC;;OAEG;IACG,uBAAuB,CAC3B,OAAO,EAAE,MAAM,GACd,OAAO,CAAC,uBAAuB,CAAC;IAiFnC;;OAEG;IACH,qBAAqB,CAAC,MAAM,EAAE,iBAAiB,GAAG,gBAAgB;IAoJlE;;OAEG;IACH,yBAAyB,CAAC,QAAQ,EAAE,MAAM,GAAG,gBAAgB;IAwC7D;;OAEG;IACH,uBAAuB,IAAI,iBAAiB,GAAG,IAAI;IAInD;;;OAGG;IACH,kBAAkB,CAAC,GAAG,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,GAAG,IAAI;IAIrD;;OAEG;IACH,kBAAkB,IAAI,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC;IAQ5C;;;;;;;;;;OAUG;IACH,oBAAoB,CAClB,MAAM,CAAC,EAAE,MAAM,EACf,OAAO,CAAC,EAAE,MAAM,EAChB,cAAc,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,EACvC,YAAY,CAAC,EAAE,aAAa,CAAC,cAAc,CAAC,EAC5C,KAAK,CAAC,EAAE,aAAa,CAAC,OAAO,CAAC,GAC7B,aAAa;IA+EhB;;;;;;;;OAQG;IACH,kBAAkB,CAChB,KAAK,CAAC,EAAE,MAAM,EACd,SAAS,CAAC,EAAE,MAAM,EAClB,SAAS,CAAC,EAAE,MAAM,EAClB,cAAc,CAAC,EAAE,cAAc,GAC9B,WAAW;IAmCd;;;;;OAKG;IACH,qBAAqB,CAAC,gBAAgB,CAAC,EAAE,MAAM,GAAG,MAAM;IAyBxD;;;;;OAKG;IACH,eAAe,CAAC,mBAAmB,CAAC,EAAE,MAAM,GAAG,MAAM,GAAG,SAAS;IAmBjE;;;;OAIG;IACH,wBAAwB,IAAI,OAAO;IAiBnC;;;;;OAKG;IACH,sBAAsB,CAAC,gBAAgB,CAAC,EAAE,MAAM,GAAG,MAAM;IAyBzD;;OAEG;IACH,qBAAqB,CAAC,OAAO,EAAE,MAAM,GAAG,kBAAkB;IAY1D;;OAEG;IACG,cAAc,CAAC,OAAO,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC;IAoClE;;OAEG;IACG,mBAAmB,CACvB,OAAO,EAAE,MAAM,EACf,KAAK,EAAE,KAAK,EACZ,QAAQ,EAAE,MAAM,EAChB,OAAO,EAAE,OAAO,GACf,OAAO,CAAC,IAAI,CAAC;IAuChB;;OAEG;IACG,mBAAmB,CACvB,OAAO,EAAE,MAAM,EACf,KAAK,EAAE,KAAK,EACZ,QAAQ,EAAE,MAAM,GACf,OAAO,CAAC,IAAI,CAAC;IAmChB;;OAEG;IACH,uBAAuB,CAAC,OAAO,EAAE,MAAM,GAAG,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC;IAKjE;;;OAGG;IACH,sBAAsB,CAAC,QAAQ,EAAE,MAAM,GAAG,iBAAiB,GAAG,IAAI;CAGnE;AAKD;;GAEG;AACH,wBAAgB,yBAAyB,CACvC,GAAG,EAAE,OAAO,EACZ,UAAU,CAAC,EAAE,MAAM,GAClB,2BAA2B,CAsD7B;AAED;;GAEG;AACH,wBAAgB,sBAAsB,CACpC,OAAO,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,GAAG,SAAS,EAC3C,UAAU,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,GAAG,SAAS,EAC9C,OAAO,GAAE,uBAA4B,GACpC,wBAAwB,CAoC1B;AAED;;;GAGG;AACH,wBAAgB,sBAAsB,CACpC,QAAQ,EAAE,MAAM,GACf,iBAAiB,GAAG,IAAI,CAmD1B;AAED;;;GAGG;AACH,wBAAgB,uBAAuB,CACrC,SAAS,EAAE,MAAM,EAAE,GAClB,iBAAiB,GAAG,IAAI,CAQ1B;AAED;;;GAGG;AACH,wBAAgB,kBAAkB,IAAI,iBAAiB,GAAG,IAAI,CAE7D;AAED;;;GAGG;AACH,wBAAgB,qBAAqB,CACnC,OAAO,EAAE,MAAM,GACd,iBAAiB,GAAG,IAAI,CAE1B;AAED;;;;GAIG;AACH,wBAAgB,oBAAoB,CAClC,OAAO,EAAE,MAAM,GACd,iBAAiB,GAAG,IAAI,CAqI1B"}
+{"version":3,"file":"configurationService.d.ts","sourceRoot":"","sources":["../../src/services/configurationService.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAKH,OAAO,KAAK,EACV,uBAAuB,EACvB,gBAAgB,EAChB,kBAAkB,EAClB,iBAAiB,EACjB,KAAK,EACN,MAAM,2BAA2B,CAAC;AAOnC,OAAO,EACL,KAAK,2BAA2B,EAChC,KAAK,wBAAwB,EAC7B,KAAK,uBAAuB,EAE7B,MAAM,yBAAyB,CAAC;AACjC,OAAO,EACL,aAAa,EACb,WAAW,EAGX,cAAc,EACd,YAAY,EACb,MAAM,mBAAmB,CAAC;AAK3B,OAAO,EAAE,aAAa,EAAE,MAAM,QAAQ,CAAC;AAGvC;;;;;GAKG;AACH,qBAAa,oBAAoB;IAC/B,OAAO,CAAC,oBAAoB,CAAkC;IAC9D,OAAO,CAAC,GAAG,CAA8B;IACzC,OAAO,CAAC,OAAO,CAAoB;IAEnC;;OAEG;IACH,UAAU,CAAC,OAAO,EAAE,YAAY,GAAG,IAAI;IAMvC;;OAEG;IACG,uBAAuB,CAC3B,OAAO,EAAE,MAAM,GACd,OAAO,CAAC,uBAAuB,CAAC;IA4DnC;;OAEG;IACH,qBAAqB,CAAC,MAAM,EAAE,iBAAiB,GAAG,gBAAgB;IAoJlE;;OAEG;IACH,yBAAyB,CAAC,QAAQ,EAAE,MAAM,GAAG,gBAAgB;IAwC7D;;;OAGG;IACH,kBAAkB,CAAC,GAAG,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,GAAG,IAAI;IAIrD;;OAEG;IACH,kBAAkB,IAAI,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC;IAQ5C;;;;;;;;;;OAUG;IACH,oBAAoB,CAClB,MAAM,CAAC,EAAE,MAAM,EACf,OAAO,CAAC,EAAE,MAAM,EAChB,cAAc,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,EACvC,YAAY,CAAC,EAAE,aAAa,CAAC,cAAc,CAAC,EAC5C,KAAK,CAAC,EAAE,aAAa,CAAC,OAAO,CAAC,GAC7B,aAAa;IAqEhB;;;;;;;;OAQG;IACH,kBAAkB,CAChB,KAAK,CAAC,EAAE,MAAM,EACd,SAAS,CAAC,EAAE,MAAM,EAClB,SAAS,CAAC,EAAE,MAAM,EAClB,cAAc,CAAC,EAAE,cAAc,GAC9B,WAAW;IA6Bd;;;;;OAKG;IACH,qBAAqB,CAAC,gBAAgB,CAAC,EAAE,MAAM,GAAG,MAAM;IAyBxD;;;;;OAKG;IACH,eAAe,CAAC,mBAAmB,CAAC,EAAE,MAAM,GAAG,MAAM,GAAG,SAAS;IAmBjE;;;;OAIG;IACH,wBAAwB,IAAI,OAAO;IAiBnC;;;;;OAKG;IACH,sBAAsB,CAAC,gBAAgB,CAAC,EAAE,MAAM,GAAG,MAAM;IAyBzD;;OAEG;IACH,qBAAqB,CAAC,OAAO,EAAE,MAAM,GAAG,kBAAkB;IAY1D;;OAEG;IACG,cAAc,CAAC,OAAO,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC;IAoClE;;OAEG;IACG,mBAAmB,CACvB,OAAO,EAAE,MAAM,EACf,KAAK,EAAE,KAAK,EACZ,QAAQ,EAAE,MAAM,EAChB,OAAO,EAAE,OAAO,GACf,OAAO,CAAC,IAAI,CAAC;IAuChB;;OAEG;IACG,mBAAmB,CACvB,OAAO,EAAE,MAAM,EACf,KAAK,EAAE,KAAK,EACZ,QAAQ,EAAE,MAAM,GACf,OAAO,CAAC,IAAI,CAAC;IAmChB;;OAEG;IACH,uBAAuB,CAAC,OAAO,EAAE,MAAM,GAAG,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC;IAKjE;;;OAGG;IACH,sBAAsB,CAAC,QAAQ,EAAE,MAAM,GAAG,iBAAiB,GAAG,IAAI;CAGnE;AAKD;;GAEG;AACH,wBAAgB,yBAAyB,CACvC,GAAG,EAAE,OAAO,EACZ,UAAU,CAAC,EAAE,MAAM,GAClB,2BAA2B,CAsD7B;AAED;;GAEG;AACH,wBAAgB,sBAAsB,CACpC,OAAO,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,GAAG,SAAS,EAC3C,UAAU,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,GAAG,SAAS,EAC9C,OAAO,GAAE,uBAA4B,GACpC,wBAAwB,CAoC1B;AAED;;;GAGG;AACH,wBAAgB,sBAAsB,CACpC,QAAQ,EAAE,MAAM,GACf,iBAAiB,GAAG,IAAI,CA4B1B;AAED;;;;GAIG;AACH,wBAAgB,oBAAoB,CAClC,OAAO,EAAE,MAAM,GACd,iBAAiB,GAAG,IAAI,CAoI1B"}

package/dist/services/configurationService.js

@@ -36,41 +36,27 @@ export class ConfigurationService {
      */
     async loadMergedConfiguration(workdir) {
         try {
-            const userConfigPaths = getUserConfigPaths();
-            const projectConfigPaths = getProjectConfigPaths(workdir);
             // Use the merged configuration function (this loads user and project configs internally)
             const mergedConfig = loadMergedWaveConfig(workdir);
-            // Track loading context for better error messages by checking which files exist
-            const loadingContext = [];
-            const userPath = userConfigPaths.find((path) => existsSync(path));
-            if (userPath) {
-                loadingContext.push(`user config from ${userPath}`);
-            }
-            const projectPath = projectConfigPaths.find((path) => existsSync(path));
-            if (projectPath) {
-                loadingContext.push(`project config from ${projectPath}`);
-            }
             if (!mergedConfig) {
-                const message = loadingContext.length > 0
-                    ? `No valid configuration found despite attempting to load: ${loadingContext.join(", ")}`
-                    : "No configuration files found in user or project directories";
                 // Still set system environment variables even if no config is found
                 const env = { WAVE_PROJECT_DIR: workdir };
                 this.setEnvironmentVars(env);
                 return {
                     configuration: { env },
                     success: true, // No config is valid
-                    warnings: [message],
+                    warnings: [
+                        "No configuration files found in user or project directories",
+                    ],
                 };
             }
             // Comprehensive validation
             const validation = this.validateConfiguration(mergedConfig);
             if (!validation.isValid) {
-                const sourcePaths = loadingContext.join(" and ");
                 return {
                     configuration: null,
                     success: false,
-                    error: `Merged configuration validation failed (sources: ${sourcePaths}): ${validation.errors.join(", ")}`,
+                    error: `Merged configuration validation failed: ${validation.errors.join(", ")}`,
                     warnings: validation.warnings,
                 };
             }
@@ -83,11 +69,10 @@ export class ConfigurationService {
             };
             this.setEnvironmentVars(env);
             mergedConfig.env = env;
-            const sourcePaths = loadingContext.join(" and ");
             return {
                 configuration: mergedConfig,
                 success: true,
-                sourcePath: sourcePaths || "merged configuration",
+                sourcePath: "merged configuration",
                 warnings: validation.warnings,
             };
         }
@@ -260,12 +245,6 @@ export class ConfigurationService {
         return result;
     }
     // Utility operations
-    /**
-     * Get currently loaded configuration
-     */
-    getCurrentConfiguration() {
-        return this.currentConfiguration;
-    }
     /**
      * Set environment variables from configuration
      * This replaces direct process.env modification
@@ -318,15 +297,6 @@ export class ConfigurationService {
         else {
             resolvedBaseURL = this.env.WAVE_BASE_URL || "";
         }
-        // If we have a parent configuration, use it as a fallback for API key and base URL
-        if (this.currentConfiguration?.env) {
-            if (resolvedApiKey === undefined) {
-                resolvedApiKey = this.currentConfiguration.env.WAVE_API_KEY;
-            }
-            if (!resolvedBaseURL) {
-                resolvedBaseURL = this.currentConfiguration.env.WAVE_BASE_URL || "";
-            }
-        }
         // Fallback to process.env if still not resolved (for dynamic updates in tests)
         if (resolvedApiKey === undefined) {
             resolvedApiKey = process.env.WAVE_API_KEY;
@@ -376,16 +346,10 @@ export class ConfigurationService {
         const DEFAULT_FAST_MODEL = "gemini-2.5-flash";
         // Resolve agent model: override > options > env (settings.json) > process.env > default
         let resolvedAgentModel = model || this.options.model || this.env.WAVE_MODEL;
-        if (!resolvedAgentModel && this.currentConfiguration?.env?.WAVE_MODEL) {
-            resolvedAgentModel = this.currentConfiguration.env.WAVE_MODEL;
-        }
         resolvedAgentModel =
             resolvedAgentModel || process.env.WAVE_MODEL || DEFAULT_AGENT_MODEL;
         // Resolve fast model: override > options > env (settings.json) > process.env > default
         let resolvedFastModel = fastModel || this.options.fastModel || this.env.WAVE_FAST_MODEL;
-        if (!resolvedFastModel && this.currentConfiguration?.env?.WAVE_FAST_MODEL) {
-            resolvedFastModel = this.currentConfiguration.env.WAVE_FAST_MODEL;
-        }
         resolvedFastModel =
             resolvedFastModel || process.env.WAVE_FAST_MODEL || DEFAULT_FAST_MODEL;
         // Resolve max output tokens
@@ -502,7 +466,7 @@ export class ConfigurationService {
         };
     }
     /**
-     * Add a permission rule to the project's settings.local.json
+     * Add a permission rule to the local settings.local.json
      */
     async addAllowedRule(workdir, rule) {
         const localConfigPath = path.join(workdir, ".wave", "settings.local.json");
@@ -541,13 +505,13 @@ export class ConfigurationService {
         }
         let configPath;
         if (scope === "user") {
-            configPath = getUserConfigPaths()[1]; // settings.json
+            configPath = getUserConfigPaths()[0]; // settings.json
         }
         else if (scope === "project") {
             configPath = getProjectConfigPaths(workdir)[1]; // settings.json
         }
         else {
-            configPath = getProjectConfigPaths(workdir)[0]; // settings.local.json
+            configPath = getProjectConfigPaths(workdir)[0]; // local settings.local.json
         }
         // Ensure directory exists
         const configDir = path.dirname(configPath);
@@ -579,13 +543,13 @@ export class ConfigurationService {
         }
         let configPath;
         if (scope === "user") {
-            configPath = getUserConfigPaths()[1]; // settings.json
+            configPath = getUserConfigPaths()[0]; // settings.json
         }
         else if (scope === "project") {
             configPath = getProjectConfigPaths(workdir)[1]; // settings.json
         }
         else {
-            configPath = getProjectConfigPaths(workdir)[0]; // settings.local.json
+            configPath = getProjectConfigPaths(workdir)[0]; // local settings.local.json
         }
         if (!existsSync(configPath)) {
             return; // Nothing to remove
@@ -710,21 +674,6 @@ export function loadWaveConfigFromFile(filePath) {
     try {
         const content = readFileSync(filePath, "utf-8");
         const config = JSON.parse(content);
-        // Validate basic structure
-        if (!config || typeof config !== "object") {
-            throw new Error(`Invalid configuration structure in ${filePath}`);
-        }
-        // Validate environment variables if present
-        if (config.env !== undefined) {
-            const envValidation = validateEnvironmentConfig(config.env, filePath);
-            if (!envValidation.isValid) {
-                throw new Error(`Environment variable validation failed in ${filePath}: ${envValidation.errors.join(", ")}`);
-            }
-            // Log warnings if any
-            if (envValidation.warnings.length > 0) {
-                console.warn(`Environment variable warnings in ${filePath}:\n- ${envValidation.warnings.join("\n- ")}`);
-            }
-        }
         return {
             hooks: config.hooks || undefined,
             env: config.env || undefined,
@@ -744,48 +693,20 @@ export function loadWaveConfigFromFile(filePath) {
         throw error;
     }
 }
-/**
- * Load Wave configuration from multiple file paths in priority order
- * Returns the first valid configuration found, or null if none exist
- */
-export function loadWaveConfigFromFiles(filePaths) {
-    for (const filePath of filePaths) {
-        const config = loadWaveConfigFromFile(filePath);
-        if (config !== null) {
-            return config;
-        }
-    }
-    return null;
-}
-/**
- * Load user-specific Wave configuration
- * Checks .local.json first, then falls back to .json
- */
-export function loadUserWaveConfig() {
-    return loadWaveConfigFromFiles(getUserConfigPaths());
-}
-/**
- * Load project-specific Wave configuration
- * Checks .local.json first, then falls back to .json
- */
-export function loadProjectWaveConfig(workdir) {
-    return loadWaveConfigFromFiles(getProjectConfigPaths(workdir));
-}
 /**
  * Load and merge Wave configuration from both user and project sources
  * Project configuration takes precedence over user configuration
  * Checks .local.json files first, then falls back to .json files
  */
 export function loadMergedWaveConfig(workdir) {
-    const userPaths = getUserConfigPaths(); // [local, json]
+    const userPaths = getUserConfigPaths(); // [json]
     const projectPaths = getProjectConfigPaths(workdir); // [local, json]
     // Priority order (lowest to highest):
-    // user settings.json -> user settings.local.json -> project settings.json -> project settings.local.json
+    // user settings.json -> project settings.json -> local settings.local.json
     const pathsToLoad = [
-        userPaths[1], // user settings.json
-        userPaths[0], // user settings.local.json
+        userPaths[0], // user settings.json
         projectPaths[1], // project settings.json
-        projectPaths[0], // project settings.local.json
+        projectPaths[0], // local settings.local.json
     ];
     const configs = [];
     for (const path of pathsToLoad) {

package/dist/services/initializationService.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"initializationService.d.ts","sourceRoot":"","sources":["../../src/services/initializationService.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EACV,OAAO,EACP,MAAM,EACN,YAAY,EACZ,WAAW,EACZ,MAAM,mBAAmB,CAAC;AAC3B,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,6BAA6B,CAAC;AAChE,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,gCAAgC,CAAC;AACtE,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,uBAAuB,CAAC;AACvD,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,4BAA4B,CAAC;AAC9D,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,8BAA8B,CAAC;AAClE,OAAO,KAAK,EAAE,mBAAmB,EAAE,MAAM,oCAAoC,CAAC;AAC9E,OAAO,KAAK,EAAE,UAAU,EAAE,MAAM,2BAA2B,CAAC;AAC5D,OAAO,KAAK,EAAE,oBAAoB,EAAE,MAAM,2BAA2B,CAAC;AACtE,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,4BAA4B,CAAC;AAC9D,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,+BAA+B,CAAC;AACpE,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,kCAAkC,CAAC;AAC1E,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,kCAAkC,CAAC;AAC1E,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,kBAAkB,CAAC;AAIpD,MAAM,WAAW,qBAAqB;IACpC,YAAY,EAAE,YAAY,CAAC;IAC3B,eAAe,EAAE,eAAe,CAAC;IACjC,SAAS,EAAE,SAAS,CAAC;IACrB,WAAW,EAAE,WAAW,CAAC;IACzB,aAAa,EAAE,aAAa,CAAC;IAC7B,OAAO,EAAE,YAAY,CAAC;IACtB,mBAAmB,EAAE,mBAAmB,CAAC;IACzC,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,UAAU,EAAE,UAAU,CAAC;IACvB,OAAO,EAAE,MAAM,CAAC;IAChB,UAAU,EAAE,WAAW,CAAC;IACxB,oBAAoB,EAAE,oBAAoB,CAAC;IAC3C,WAAW,EAAE,WAAW,CAAC;IACzB,cAAc,EAAE,cAAc,CAAC;IAC/B,iBAAiB,EAAE,iBAAiB,CAAC;IACrC,iBAAiB,EAAE,iBAAiB,CAAC;IACrC,WAAW,EAAE,WAAW,CAAC;IACzB,gBAAgB,EAAE,CAAC,OAAO,EAAE,MAAM,KAAK,IAAI,CAAC;IAC5C,aAAa,EAAE,CAAC,OAAO,EAAE,MAAM,KAAK,IAAI,CAAC;IACzC,wBAAwB,EAAE,MAAM,IAAI,CAAC;CACtC;AAED,qBAAa,qBAAqB;WACZ,UAAU,CAC5B,OAAO,EAAE,qBAAqB,EAC9B,OAAO,CAAC,EAAE;QACR,gBAAgB,CAAC,EAAE,MAAM,CAAC;QAC1B,mBAAmB,CAAC,EAAE,OAAO,CAAC;QAC9B,QAAQ,CAAC,EAAE,OAAO,EAAE,CAAC;KACtB,GACA,OAAO,CAAC,IAAI,CAAC;CAqOjB"}
+{"version":3,"file":"initializationService.d.ts","sourceRoot":"","sources":["../../src/services/initializationService.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EACV,OAAO,EACP,MAAM,EACN,YAAY,EACZ,WAAW,EACZ,MAAM,mBAAmB,CAAC;AAC3B,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,6BAA6B,CAAC;AAChE,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,gCAAgC,CAAC;AACtE,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,uBAAuB,CAAC;AACvD,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,4BAA4B,CAAC;AAC9D,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,8BAA8B,CAAC;AAClE,OAAO,KAAK,EAAE,mBAAmB,EAAE,MAAM,oCAAoC,CAAC;AAC9E,OAAO,KAAK,EAAE,UAAU,EAAE,MAAM,2BAA2B,CAAC;AAC5D,OAAO,KAAK,EAAE,oBAAoB,EAAE,MAAM,2BAA2B,CAAC;AACtE,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,4BAA4B,CAAC;AAC9D,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,+BAA+B,CAAC;AACpE,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,kCAAkC,CAAC;AAC1E,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,kCAAkC,CAAC;AAC1E,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,kBAAkB,CAAC;AAIpD,MAAM,WAAW,qBAAqB;IACpC,YAAY,EAAE,YAAY,CAAC;IAC3B,eAAe,EAAE,eAAe,CAAC;IACjC,SAAS,EAAE,SAAS,CAAC;IACrB,WAAW,EAAE,WAAW,CAAC;IACzB,aAAa,EAAE,aAAa,CAAC;IAC7B,OAAO,EAAE,YAAY,CAAC;IACtB,mBAAmB,EAAE,mBAAmB,CAAC;IACzC,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,UAAU,EAAE,UAAU,CAAC;IACvB,OAAO,EAAE,MAAM,CAAC;IAChB,UAAU,EAAE,WAAW,CAAC;IACxB,oBAAoB,EAAE,oBAAoB,CAAC;IAC3C,WAAW,EAAE,WAAW,CAAC;IACzB,cAAc,EAAE,cAAc,CAAC;IAC/B,iBAAiB,EAAE,iBAAiB,CAAC;IACrC,iBAAiB,EAAE,iBAAiB,CAAC;IACrC,WAAW,EAAE,WAAW,CAAC;IACzB,gBAAgB,EAAE,CAAC,OAAO,EAAE,MAAM,KAAK,IAAI,CAAC;IAC5C,aAAa,EAAE,CAAC,OAAO,EAAE,MAAM,KAAK,IAAI,CAAC;IACzC,wBAAwB,EAAE,MAAM,IAAI,CAAC;CACtC;AAED,qBAAa,qBAAqB;WACZ,UAAU,CAC5B,OAAO,EAAE,qBAAqB,EAC9B,OAAO,CAAC,EAAE;QACR,gBAAgB,CAAC,EAAE,MAAM,CAAC;QAC1B,mBAAmB,CAAC,EAAE,OAAO,CAAC;QAC9B,QAAQ,CAAC,EAAE,OAAO,EAAE,CAAC;KACtB,GACA,OAAO,CAAC,IAAI,CAAC;CAgPjB"}

package/dist/services/initializationService.js

@@ -57,6 +57,9 @@ export class InitializationService {
                     if (configResult.configuration.permissions.defaultMode) {
                         permissionManager.updateConfiguredDefaultMode(configResult.configuration.permissions.defaultMode);
                     }
+                    if (configResult.configuration.permissions.additionalDirectories) {
+                        permissionManager.updateAdditionalDirectories(configResult.configuration.permissions.additionalDirectories);
+                    }
                 }
             }
         }
@@ -93,6 +96,11 @@ export class InitializationService {
                 const memoryService = container.get("MemoryService");
                 if (memoryService) {
                     await memoryService.ensureAutoMemoryDirectory(workdir);
+                    const permissionManager = container.get("PermissionManager");
+                    if (permissionManager) {
+                        const autoMemoryDir = memoryService.getAutoMemoryDirectory(workdir);
+                        permissionManager.addSystemAdditionalDirectory(autoMemoryDir);
+                    }
                 }
             }
         }

package/dist/services/memory.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"memory.d.ts","sourceRoot":"","sources":["../../src/services/memory.ts"],"names":[],"mappings":"AAKA,OAAO,EAAE,SAAS,EAAE,MAAM,uBAAuB,CAAC;AAIlD,qBAAa,aAAa;IACZ,OAAO,CAAC,SAAS;gBAAT,SAAS,EAAE,SAAS;IAExC;;;OAGG;IACH,sBAAsB,CAAC,OAAO,EAAE,MAAM,GAAG,MAAM;IAM/C;;OAEG;IACG,yBAAyB,CAAC,OAAO,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC;IA2B/D;;OAEG;IACG,oBAAoB,CAAC,OAAO,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC;IAiBtD,oBAAoB,IAAI,OAAO,CAAC,IAAI,CAAC;IA8BrC,oBAAoB,IAAI,OAAO,CAAC,MAAM,CAAC;IAevC,cAAc,CAAC,OAAO,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC;IAuBhD,wBAAwB,CAAC,OAAO,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC;CAqBjE"}
+{"version":3,"file":"memory.d.ts","sourceRoot":"","sources":["../../src/services/memory.ts"],"names":[],"mappings":"AAKA,OAAO,EAAE,SAAS,EAAE,MAAM,uBAAuB,CAAC;AAIlD,qBAAa,aAAa;IACZ,OAAO,CAAC,SAAS;gBAAT,SAAS,EAAE,SAAS;IAExC;;;OAGG;IACH,sBAAsB,CAAC,OAAO,EAAE,MAAM,GAAG,MAAM;IAU/C;;OAEG;IACG,yBAAyB,CAAC,OAAO,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC;IA2B/D;;OAEG;IACG,oBAAoB,CAAC,OAAO,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC;IAiBtD,oBAAoB,IAAI,OAAO,CAAC,IAAI,CAAC;IA8BrC,oBAAoB,IAAI,OAAO,CAAC,MAAM,CAAC;IAevC,cAAc,CAAC,OAAO,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC;IAuBhD,wBAAwB,CAAC,OAAO,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC;CAqBjE"}

package/dist/services/memory.js

@@ -14,7 +14,10 @@ export class MemoryService {
      * Uses the git common directory to ensure worktrees share the same memory.
      */
     getAutoMemoryDirectory(workdir) {
-        const projectRoot = getGitCommonDir(workdir);
+        const commonDir = getGitCommonDir(workdir);
+        // If the common directory is a .git directory, use its parent as the project root
+        // for a cleaner encoded name while maintaining stability across worktrees.
+        const projectRoot = path.basename(commonDir) === ".git" ? path.dirname(commonDir) : commonDir;
         const encodedName = pathEncoder.encodeSync(projectRoot);
         return path.join(homedir(), ".wave", "projects", encodedName, "memory");
     }