@ncukondo/reference-manager 0.1.0 → 0.4.0

package/dist/config/csl-styles.d.ts

@@ -0,0 +1,83 @@
+/**
+ * CSL Style Management
+ *
+ * Handles resolution and loading of CSL (Citation Style Language) style files.
+ *
+ * Style Resolution Order:
+ * 1. --csl-file <path> (exact file path)
+ * 2. Built-in style matching --style <name>
+ * 3. Search in csl_directory paths (in array order)
+ * 4. Default style from config (default_style)
+ * 5. "apa" (hardcoded default)
+ */
+/**
+ * Built-in styles available in @citation-js/plugin-csl
+ * These can be used directly without loading external files
+ */
+export declare const BUILTIN_STYLES: readonly ["apa", "vancouver", "harvard"];
+export type BuiltinStyleName = (typeof BUILTIN_STYLES)[number];
+/**
+ * Check if a style name is a built-in style
+ */
+export declare function isBuiltinStyle(styleName: string): styleName is BuiltinStyleName;
+export interface StyleResolutionOptions {
+    /**
+     * Exact path to CSL file (from --csl-file option)
+     * Takes highest priority
+     */
+    cslFile?: string;
+    /**
+     * Style name to resolve (from --style option)
+     */
+    style?: string;
+    /**
+     * Directory or directories to search for custom CSL files
+     * (from csl_directory config)
+     * Can be a single string or array of strings
+     */
+    cslDirectory?: string | string[];
+    /**
+     * Default style to use if specified style not found
+     * (from default_style config)
+     */
+    defaultStyle?: string;
+}
+export interface StyleResolution {
+    /**
+     * Type of resolution: "builtin" for citation-js built-in styles,
+     * "custom" for external CSL files
+     */
+    type: "builtin" | "custom";
+    /**
+     * The resolved style name (for built-in) or identifier (for custom)
+     */
+    styleName: string;
+    /**
+     * CSL XML content (only for custom styles)
+     */
+    styleXml?: string;
+}
+/**
+ * Load CSL style file content from the given path
+ *
+ * @param stylePath - Path to the CSL style file
+ * @returns Content of the CSL style file (XML string)
+ * @throws Error if file cannot be read
+ */
+export declare function loadCSLStyleFile(stylePath: string): string;
+/**
+ * Resolve the style based on resolution options
+ *
+ * Resolution order:
+ * 1. cslFile (exact path) - throws if doesn't exist
+ * 2. Built-in style matching style name
+ * 3. Search in csl_directory paths (in order)
+ * 4. Default style (defaultStyle) - if built-in
+ * 5. "apa" (hardcoded fallback)
+ *
+ * @param options - Style resolution options
+ * @returns StyleResolution with type, styleName, and optional styleXml
+ * @throws Error if cslFile is specified but doesn't exist
+ */
+export declare function resolveStyle(options: StyleResolutionOptions): StyleResolution;
+//# sourceMappingURL=csl-styles.d.ts.map

package/dist/config/csl-styles.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"csl-styles.d.ts","sourceRoot":"","sources":["../../src/config/csl-styles.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAKH;;;GAGG;AACH,eAAO,MAAM,cAAc,0CAA2C,CAAC;AAEvE,MAAM,MAAM,gBAAgB,GAAG,CAAC,OAAO,cAAc,CAAC,CAAC,MAAM,CAAC,CAAC;AAE/D;;GAEG;AACH,wBAAgB,cAAc,CAAC,SAAS,EAAE,MAAM,GAAG,SAAS,IAAI,gBAAgB,CAE/E;AAED,MAAM,WAAW,sBAAsB;IACrC;;;OAGG;IACH,OAAO,CAAC,EAAE,MAAM,CAAC;IAEjB;;OAEG;IACH,KAAK,CAAC,EAAE,MAAM,CAAC;IAEf;;;;OAIG;IACH,YAAY,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE,CAAC;IAEjC;;;OAGG;IACH,YAAY,CAAC,EAAE,MAAM,CAAC;CACvB;AAED,MAAM,WAAW,eAAe;IAC9B;;;OAGG;IACH,IAAI,EAAE,SAAS,GAAG,QAAQ,CAAC;IAE3B;;OAEG;IACH,SAAS,EAAE,MAAM,CAAC;IAElB;;OAEG;IACH,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAaD;;;;;;GAMG;AACH,wBAAgB,gBAAgB,CAAC,SAAS,EAAE,MAAM,GAAG,MAAM,CAE1D;AAED;;;;;;;;;;;;;GAaG;AACH,wBAAgB,YAAY,CAAC,OAAO,EAAE,sBAAsB,GAAG,eAAe,CA4D7E"}

package/dist/config/defaults.d.ts

@@ -22,6 +22,16 @@ export declare function getDefaultUserConfigPath(): string;
  * Uses .reference-manager.config.toml
  */
 export declare function getDefaultCurrentDirConfigFilename(): string;
+/**
+ * Get the default CSL directory
+ * Uses ~/.reference-manager/csl/
+ */
+export declare function getDefaultCslDirectory(): string;
+/**
+ * Get the default fulltext directory
+ * Uses ~/.reference-manager/fulltext/
+ */
+export declare function getDefaultFulltextDirectory(): string;
 /**
  * Default configuration
  */

package/dist/config/defaults.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"defaults.d.ts","sourceRoot":"","sources":["../../src/config/defaults.ts"],"names":[],"mappings":"AAAA;;GAEG;AAKH,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,aAAa,CAAC;AAE1C;;;GAGG;AACH,wBAAgB,yBAAyB,IAAI,MAAM,CAElD;AAED;;;GAGG;AACH,wBAAgB,qBAAqB,IAAI,MAAM,CAE9C;AAED;;;GAGG;AACH,wBAAgB,wBAAwB,IAAI,MAAM,CAEjD;AAED;;;GAGG;AACH,wBAAgB,kCAAkC,IAAI,MAAM,CAE3D;AAED;;GAEG;AACH,eAAO,MAAM,aAAa,EAAE,MAmB3B,CAAC"}
+{"version":3,"file":"defaults.d.ts","sourceRoot":"","sources":["../../src/config/defaults.ts"],"names":[],"mappings":"AAAA;;GAEG;AAKH,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,aAAa,CAAC;AAE1C;;;GAGG;AACH,wBAAgB,yBAAyB,IAAI,MAAM,CAElD;AAED;;;GAGG;AACH,wBAAgB,qBAAqB,IAAI,MAAM,CAE9C;AAED;;;GAGG;AACH,wBAAgB,wBAAwB,IAAI,MAAM,CAEjD;AAED;;;GAGG;AACH,wBAAgB,kCAAkC,IAAI,MAAM,CAE3D;AAED;;;GAGG;AACH,wBAAgB,sBAAsB,IAAI,MAAM,CAE/C;AAED;;;GAGG;AACH,wBAAgB,2BAA2B,IAAI,MAAM,CAEpD;AAED;;GAEG;AACH,eAAO,MAAM,aAAa,EAAE,MA+B3B,CAAC"}

package/dist/config/loader.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"loader.d.ts","sourceRoot":"","sources":["../../src/config/loader.ts"],"names":[],"mappings":"AAAA;;GAEG;AAUH,OAAO,EACL,KAAK,MAAM,EAMZ,MAAM,aAAa,CAAC;AAErB;;GAEG;AACH,MAAM,WAAW,iBAAiB;IAChC,yDAAyD;IACzD,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,mEAAmE;IACnE,cAAc,CAAC,EAAE,MAAM,CAAC;IACxB,6BAA6B;IAC7B,SAAS,CAAC,EAAE,OAAO,CAAC,MAAM,CAAC,CAAC;CAC7B;AAmGD;;;;;;;;;GASG;AACH,wBAAgB,UAAU,CAAC,OAAO,GAAE,iBAAsB,GAAG,MAAM,CAwClE"}
+{"version":3,"file":"loader.d.ts","sourceRoot":"","sources":["../../src/config/loader.ts"],"names":[],"mappings":"AAAA;;GAEG;AAWH,OAAO,EACL,KAAK,MAAM,EAMZ,MAAM,aAAa,CAAC;AAErB;;GAEG;AACH,MAAM,WAAW,iBAAiB;IAChC,yDAAyD;IACzD,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,mEAAmE;IACnE,cAAc,CAAC,EAAE,MAAM,CAAC;IACxB,6BAA6B;IAC7B,SAAS,CAAC,EAAE,OAAO,CAAC,MAAM,CAAC,CAAC;CAC7B;AA8ID;;;;;;;;;GASG;AACH,wBAAgB,UAAU,CAAC,OAAO,GAAE,iBAAsB,GAAG,MAAM,CAwClE"}

package/dist/config/schema.d.ts

@@ -20,9 +20,10 @@ export declare const backupConfigSchema: z.ZodObject<{
 }, z.core.$strip>;
 /**
  * File watching configuration schema
+ * Note: File watching is always enabled in server mode (HTTP/MCP).
+ * CLI mode does not use file watching.
  */
 export declare const watchConfigSchema: z.ZodObject<{
-    enabled: z.ZodBoolean;
     debounceMs: z.ZodNumber;
     pollIntervalMs: z.ZodNumber;
     retryIntervalMs: z.ZodNumber;
@@ -35,6 +36,40 @@ export declare const serverConfigSchema: z.ZodObject<{
     autoStart: z.ZodBoolean;
     autoStopMinutes: z.ZodNumber;
 }, z.core.$strip>;
+/**
+ * Citation format schema
+ */
+export declare const citationFormatSchema: z.ZodEnum<{
+    text: "text";
+    html: "html";
+    rtf: "rtf";
+}>;
+/**
+ * Citation configuration schema
+ */
+export declare const citationConfigSchema: z.ZodObject<{
+    defaultStyle: z.ZodString;
+    cslDirectory: z.ZodArray<z.ZodString>;
+    defaultLocale: z.ZodString;
+    defaultFormat: z.ZodEnum<{
+        text: "text";
+        html: "html";
+        rtf: "rtf";
+    }>;
+}, z.core.$strip>;
+/**
+ * PubMed API configuration schema
+ */
+export declare const pubmedConfigSchema: z.ZodObject<{
+    email: z.ZodOptional<z.ZodString>;
+    apiKey: z.ZodOptional<z.ZodString>;
+}, z.core.$strip>;
+/**
+ * Fulltext storage configuration schema
+ */
+export declare const fulltextConfigSchema: z.ZodObject<{
+    directory: z.ZodString;
+}, z.core.$strip>;
 /**
  * Complete configuration schema
  */
@@ -51,7 +86,6 @@ export declare const configSchema: z.ZodObject<{
         directory: z.ZodString;
     }, z.core.$strip>;
     watch: z.ZodObject<{
-        enabled: z.ZodBoolean;
         debounceMs: z.ZodNumber;
         pollIntervalMs: z.ZodNumber;
         retryIntervalMs: z.ZodNumber;
@@ -61,6 +95,23 @@ export declare const configSchema: z.ZodObject<{
         autoStart: z.ZodBoolean;
         autoStopMinutes: z.ZodNumber;
     }, z.core.$strip>;
+    citation: z.ZodObject<{
+        defaultStyle: z.ZodString;
+        cslDirectory: z.ZodArray<z.ZodString>;
+        defaultLocale: z.ZodString;
+        defaultFormat: z.ZodEnum<{
+            text: "text";
+            html: "html";
+            rtf: "rtf";
+        }>;
+    }, z.core.$strip>;
+    pubmed: z.ZodObject<{
+        email: z.ZodOptional<z.ZodString>;
+        apiKey: z.ZodOptional<z.ZodString>;
+    }, z.core.$strip>;
+    fulltext: z.ZodObject<{
+        directory: z.ZodString;
+    }, z.core.$strip>;
 }, z.core.$strip>;
 /**
  * Partial configuration schema (for TOML files)
@@ -86,7 +137,6 @@ export declare const partialConfigSchema: z.ZodObject<{
         directory: z.ZodOptional<z.ZodString>;
     }, z.core.$strip>>;
     watch: z.ZodOptional<z.ZodObject<{
-        enabled: z.ZodOptional<z.ZodBoolean>;
         debounceMs: z.ZodOptional<z.ZodNumber>;
         debounce_ms: z.ZodOptional<z.ZodNumber>;
         pollIntervalMs: z.ZodOptional<z.ZodNumber>;
@@ -102,6 +152,32 @@ export declare const partialConfigSchema: z.ZodObject<{
         autoStopMinutes: z.ZodOptional<z.ZodNumber>;
         auto_stop_minutes: z.ZodOptional<z.ZodNumber>;
     }, z.core.$strip>>;
+    citation: z.ZodOptional<z.ZodObject<{
+        defaultStyle: z.ZodOptional<z.ZodString>;
+        default_style: z.ZodOptional<z.ZodString>;
+        cslDirectory: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        csl_directory: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        defaultLocale: z.ZodOptional<z.ZodString>;
+        default_locale: z.ZodOptional<z.ZodString>;
+        defaultFormat: z.ZodOptional<z.ZodEnum<{
+            text: "text";
+            html: "html";
+            rtf: "rtf";
+        }>>;
+        default_format: z.ZodOptional<z.ZodEnum<{
+            text: "text";
+            html: "html";
+            rtf: "rtf";
+        }>>;
+    }, z.core.$strip>>;
+    pubmed: z.ZodOptional<z.ZodObject<{
+        email: z.ZodOptional<z.ZodString>;
+        apiKey: z.ZodOptional<z.ZodString>;
+        api_key: z.ZodOptional<z.ZodString>;
+    }, z.core.$strip>>;
+    fulltext: z.ZodOptional<z.ZodObject<{
+        directory: z.ZodOptional<z.ZodString>;
+    }, z.core.$strip>>;
 }, z.core.$loose>;
 /**
  * Inferred types from schemas
@@ -110,6 +186,10 @@ export type LogLevel = z.infer<typeof logLevelSchema>;
 export type BackupConfig = z.infer<typeof backupConfigSchema>;
 export type WatchConfig = z.infer<typeof watchConfigSchema>;
 export type ServerConfig = z.infer<typeof serverConfigSchema>;
+export type CitationFormat = z.infer<typeof citationFormatSchema>;
+export type CitationConfig = z.infer<typeof citationConfigSchema>;
+export type PubmedConfig = z.infer<typeof pubmedConfigSchema>;
+export type FulltextConfig = z.infer<typeof fulltextConfigSchema>;
 export type Config = z.infer<typeof configSchema>;
 export type PartialConfig = z.infer<typeof partialConfigSchema>;
 /**
@@ -121,6 +201,9 @@ export type DeepPartialConfig = {
     backup?: Partial<BackupConfig>;
     watch?: Partial<WatchConfig>;
     server?: Partial<ServerConfig>;
+    citation?: Partial<CitationConfig>;
+    pubmed?: Partial<PubmedConfig>;
+    fulltext?: Partial<FulltextConfig>;
 };
 /**
  * Normalize snake_case fields to camelCase

package/dist/config/schema.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"schema.d.ts","sourceRoot":"","sources":["../../src/config/schema.ts"],"names":[],"mappings":"AAAA;;GAEG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AAExB;;GAEG;AACH,eAAO,MAAM,cAAc;;;;EAAsC,CAAC;AAElE;;GAEG;AACH,eAAO,MAAM,kBAAkB;;;;iBAI7B,CAAC;AAEH;;GAEG;AACH,eAAO,MAAM,iBAAiB;;;;;;iBAM5B,CAAC;AAEH;;GAEG;AACH,eAAO,MAAM,kBAAkB;;;iBAG7B,CAAC;AAEH;;GAEG;AACH,eAAO,MAAM,YAAY;;;;;;;;;;;;;;;;;;;;;;;iBAMvB,CAAC;AAEH;;;GAGG;AACH,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;iBAoChB,CAAC;AAEjB;;GAEG;AACH,MAAM,MAAM,QAAQ,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,cAAc,CAAC,CAAC;AACtD,MAAM,MAAM,YAAY,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,kBAAkB,CAAC,CAAC;AAC9D,MAAM,MAAM,WAAW,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,iBAAiB,CAAC,CAAC;AAC5D,MAAM,MAAM,YAAY,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,kBAAkB,CAAC,CAAC;AAC9D,MAAM,MAAM,MAAM,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,YAAY,CAAC,CAAC;AAClD,MAAM,MAAM,aAAa,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,mBAAmB,CAAC,CAAC;AAEhE;;GAEG;AACH,MAAM,MAAM,iBAAiB,GAAG;IAC9B,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,QAAQ,CAAC,EAAE,QAAQ,CAAC;IACpB,MAAM,CAAC,EAAE,OAAO,CAAC,YAAY,CAAC,CAAC;IAC/B,KAAK,CAAC,EAAE,OAAO,CAAC,WAAW,CAAC,CAAC;IAC7B,MAAM,CAAC,EAAE,OAAO,CAAC,YAAY,CAAC,CAAC;CAChC,CAAC;AAwGF;;GAEG;AACH,wBAAgB,sBAAsB,CAAC,OAAO,EAAE,aAAa,GAAG,iBAAiB,CA2ChF"}
+{"version":3,"file":"schema.d.ts","sourceRoot":"","sources":["../../src/config/schema.ts"],"names":[],"mappings":"AAAA;;GAEG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AAExB;;GAEG;AACH,eAAO,MAAM,cAAc;;;;EAAsC,CAAC;AAElE;;GAEG;AACH,eAAO,MAAM,kBAAkB;;;;iBAI7B,CAAC;AAEH;;;;GAIG;AACH,eAAO,MAAM,iBAAiB;;;;;iBAK5B,CAAC;AAEH;;GAEG;AACH,eAAO,MAAM,kBAAkB;;;iBAG7B,CAAC;AAEH;;GAEG;AACH,eAAO,MAAM,oBAAoB;;;;EAAkC,CAAC;AAEpE;;GAEG;AACH,eAAO,MAAM,oBAAoB;;;;;;;;;iBAK/B,CAAC;AAEH;;GAEG;AACH,eAAO,MAAM,kBAAkB;;;iBAG7B,CAAC;AAEH;;GAEG;AACH,eAAO,MAAM,oBAAoB;;iBAE/B,CAAC;AAEH;;GAEG;AACH,eAAO,MAAM,YAAY;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;iBASvB,CAAC;AAEH;;;GAGG;AACH,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;iBA2DhB,CAAC;AAEjB;;GAEG;AACH,MAAM,MAAM,QAAQ,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,cAAc,CAAC,CAAC;AACtD,MAAM,MAAM,YAAY,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,kBAAkB,CAAC,CAAC;AAC9D,MAAM,MAAM,WAAW,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,iBAAiB,CAAC,CAAC;AAC5D,MAAM,MAAM,YAAY,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,kBAAkB,CAAC,CAAC;AAC9D,MAAM,MAAM,cAAc,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,oBAAoB,CAAC,CAAC;AAClE,MAAM,MAAM,cAAc,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,oBAAoB,CAAC,CAAC;AAClE,MAAM,MAAM,YAAY,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,kBAAkB,CAAC,CAAC;AAC9D,MAAM,MAAM,cAAc,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,oBAAoB,CAAC,CAAC;AAClE,MAAM,MAAM,MAAM,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,YAAY,CAAC,CAAC;AAClD,MAAM,MAAM,aAAa,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,mBAAmB,CAAC,CAAC;AAEhE;;GAEG;AACH,MAAM,MAAM,iBAAiB,GAAG;IAC9B,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,QAAQ,CAAC,EAAE,QAAQ,CAAC;IACpB,MAAM,CAAC,EAAE,OAAO,CAAC,YAAY,CAAC,CAAC;IAC/B,KAAK,CAAC,EAAE,OAAO,CAAC,WAAW,CAAC,CAAC;IAC7B,MAAM,CAAC,EAAE,OAAO,CAAC,YAAY,CAAC,CAAC;IAC/B,QAAQ,CAAC,EAAE,OAAO,CAAC,cAAc,CAAC,CAAC;IACnC,MAAM,CAAC,EAAE,OAAO,CAAC,YAAY,CAAC,CAAC;IAC/B,QAAQ,CAAC,EAAE,OAAO,CAAC,cAAc,CAAC,CAAC;CACpC,CAAC;AAoKF;;GAEG;AACH,wBAAgB,sBAAsB,CAAC,OAAO,EAAE,aAAa,GAAG,iBAAiB,CAmEhF"}

package/dist/core/csl-json/types.d.ts

@@ -4,7 +4,12 @@ declare const CslCustomSchema: z.ZodObject<{
     created_at: z.ZodString;
     timestamp: z.ZodString;
     additional_urls: z.ZodOptional<z.ZodArray<z.ZodString>>;
-}, z.core.$strip>;
+    fulltext: z.ZodOptional<z.ZodObject<{
+        pdf: z.ZodOptional<z.ZodString>;
+        markdown: z.ZodOptional<z.ZodString>;
+    }, z.core.$strip>>;
+    tags: z.ZodOptional<z.ZodArray<z.ZodString>>;
+}, z.core.$loose>;
 export declare const CslItemSchema: z.ZodObject<{
     id: z.ZodString;
     type: z.ZodString;
@@ -59,7 +64,12 @@ export declare const CslItemSchema: z.ZodObject<{
         created_at: z.ZodString;
         timestamp: z.ZodString;
         additional_urls: z.ZodOptional<z.ZodArray<z.ZodString>>;
-    }, z.core.$strip>>;
+        fulltext: z.ZodOptional<z.ZodObject<{
+            pdf: z.ZodOptional<z.ZodString>;
+            markdown: z.ZodOptional<z.ZodString>;
+        }, z.core.$strip>>;
+        tags: z.ZodOptional<z.ZodArray<z.ZodString>>;
+    }, z.core.$loose>>;
 }, z.core.$loose>;
 export declare const CslLibrarySchema: z.ZodArray<z.ZodObject<{
     id: z.ZodString;
@@ -115,7 +125,12 @@ export declare const CslLibrarySchema: z.ZodArray<z.ZodObject<{
         created_at: z.ZodString;
         timestamp: z.ZodString;
         additional_urls: z.ZodOptional<z.ZodArray<z.ZodString>>;
-    }, z.core.$strip>>;
+        fulltext: z.ZodOptional<z.ZodObject<{
+            pdf: z.ZodOptional<z.ZodString>;
+            markdown: z.ZodOptional<z.ZodString>;
+        }, z.core.$strip>>;
+        tags: z.ZodOptional<z.ZodArray<z.ZodString>>;
+    }, z.core.$loose>>;
 }, z.core.$loose>>;
 export type CslCustom = z.infer<typeof CslCustomSchema>;
 export type CslItem = z.infer<typeof CslItemSchema>;

package/dist/core/csl-json/types.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"types.d.ts","sourceRoot":"","sources":["../../../src/core/csl-json/types.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AAsBxB,QAAA,MAAM,eAAe;;;;;iBAKnB,CAAC;AAGH,eAAO,MAAM,aAAa;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;iBA2BV,CAAC;AAGjB,eAAO,MAAM,gBAAgB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBAAyB,CAAC;AAEvD,MAAM,MAAM,SAAS,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,eAAe,CAAC,CAAC;AACxD,MAAM,MAAM,OAAO,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,aAAa,CAAC,CAAC;AACpD,MAAM,MAAM,UAAU,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,gBAAgB,CAAC,CAAC"}
+{"version":3,"file":"types.d.ts","sourceRoot":"","sources":["../../../src/core/csl-json/types.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AA4BxB,QAAA,MAAM,eAAe;;;;;;;;;;iBASL,CAAC;AAGjB,eAAO,MAAM,aAAa;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;iBA2BV,CAAC;AAGjB,eAAO,MAAM,gBAAgB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBAAyB,CAAC;AAEvD,MAAM,MAAM,SAAS,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,eAAe,CAAC,CAAC;AACxD,MAAM,MAAM,OAAO,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,aAAa,CAAC,CAAC;AACpD,MAAM,MAAM,UAAU,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,gBAAgB,CAAC,CAAC"}

package/dist/core/library-interface.d.ts

@@ -0,0 +1,100 @@
+/**
+ * ILibrary - Common interface for library implementations.
+ *
+ * Both Library (local file-based) and ServerClient (HTTP-based) implement this interface,
+ * allowing operations to work with either implementation interchangeably.
+ *
+ * Design notes:
+ * - All methods are async to support HTTP-based implementations (ServerClient)
+ * - Methods return CslItem directly (not Reference) for simplicity and HTTP compatibility
+ * - Library internally uses Reference for ID generation and indexing, but exposes CslItem via ILibrary
+ * - ServerClient naturally returns CslItem from HTTP responses
+ */
+import type { CslItem } from "./csl-json/types.js";
+/**
+ * Options for find operations.
+ */
+export interface FindOptions {
+    /** If true, treat the identifier as UUID; otherwise treat as citation ID (default: false) */
+    byUuid?: boolean;
+}
+/**
+ * Options for remove operations.
+ * Currently identical to FindOptions, but defined separately for clarity and future extensibility.
+ */
+export type RemoveOptions = FindOptions;
+/**
+ * Result of a remove operation.
+ */
+export interface RemoveResult {
+    /** Whether the removal was successful */
+    removed: boolean;
+    /** The removed item (only when removed=true, may be undefined if not available from server) */
+    removedItem?: CslItem;
+}
+export interface UpdateOptions {
+    /** How to handle ID collision: 'fail' (default) or 'suffix' */
+    onIdCollision?: "fail" | "suffix";
+    /** If true, treat the identifier as UUID; otherwise treat as citation ID (default: false) */
+    byUuid?: boolean;
+}
+/**
+ * Result of an update operation.
+ */
+export interface UpdateResult {
+    /** Whether the update was successful */
+    updated: boolean;
+    /** The updated item (only when updated=true) */
+    item?: CslItem;
+    /** True if ID collision occurred (only when updated=false and onIdCollision='fail') */
+    idCollision?: boolean;
+    /** True if the ID was changed due to collision resolution */
+    idChanged?: boolean;
+    /** The new ID after collision resolution (only when idChanged=true) */
+    newId?: string;
+}
+/**
+ * Common interface for library implementations.
+ */
+export interface ILibrary {
+    /**
+     * Find a reference by citation ID or UUID.
+     * @param identifier - The citation ID or UUID of the reference to find
+     * @param options - Find options (byUuid to use UUID lookup)
+     * @returns The CSL item if found, undefined otherwise
+     */
+    find(identifier: string, options?: FindOptions): Promise<CslItem | undefined>;
+    /**
+     * Get all references.
+     * @returns Array of all CSL items in the library
+     */
+    getAll(): Promise<CslItem[]>;
+    /**
+     * Add a new reference to the library.
+     * @param item - The CSL item to add
+     * @returns The added CSL item (with generated ID and UUID if not present)
+     */
+    add(item: CslItem): Promise<CslItem>;
+    /**
+     * Update a reference by citation ID or UUID.
+     * @param identifier - The citation ID or UUID of the reference to update
+     * @param updates - Partial CSL item with fields to update
+     * @param options - Update options (byUuid to use UUID lookup, onIdCollision for collision handling)
+     * @returns Update result indicating success/failure, updated item, and any ID changes
+     */
+    update(identifier: string, updates: Partial<CslItem>, options?: UpdateOptions): Promise<UpdateResult>;
+    /**
+     * Remove a reference by citation ID or UUID.
+     * @param identifier - The citation ID or UUID of the reference to remove
+     * @param options - Remove options (byUuid to use UUID lookup)
+     * @returns Remove result with removed status and optionally the removed item
+     */
+    remove(identifier: string, options?: RemoveOptions): Promise<RemoveResult>;
+    /**
+     * Save the library to persistent storage.
+     * For Library: writes to file
+     * For ServerClient: no-op (HTTP requests are already persisted)
+     */
+    save(): Promise<void>;
+}
+//# sourceMappingURL=library-interface.d.ts.map

package/dist/core/library-interface.d.ts.map

@@ -0,0 +1 @@
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package/dist/core/library.d.ts

@@ -1,9 +1,12 @@
 import type { CslItem } from "./csl-json/types";
+import type { FindOptions, ILibrary, RemoveOptions, RemoveResult, UpdateOptions, UpdateResult } from "./library-interface.js";
 import { Reference } from "./reference";
+export type { FindOptions, ILibrary, UpdateOptions, UpdateResult } from "./library-interface.js";
 /**
- * Library manager for CSL-JSON references
+ * Library manager for CSL-JSON references.
+ * Implements ILibrary interface for use with operations layer.
  */
-export declare class Library {
+export declare class Library implements ILibrary {
     private filePath;
     private references;
     private currentHash;
@@ -21,25 +24,39 @@ export declare class Library {
      */
     save(): Promise<void>;
     /**
-     * Add a reference to the library
+     * Reloads the library from file if it was modified externally.
+     * Self-writes (detected via hash comparison) are skipped.
+     * @returns true if reload occurred, false if skipped (self-write detected)
      */
-    add(item: CslItem): void;
+    reload(): Promise<boolean>;
     /**
-     * Remove a reference by UUID
+     * Add a reference to the library
+     * @param item - The CSL item to add
+     * @returns The added CSL item (with generated ID and UUID)
      */
-    removeByUuid(uuid: string): boolean;
+    add(item: CslItem): Promise<CslItem>;
     /**
-     * Remove a reference by ID
+     * Remove a reference by citation ID or UUID.
+     * @param identifier - The citation ID or UUID of the reference to remove
+     * @param options - Remove options (byUuid to use UUID lookup)
+     * @returns Remove result with removed status and the removed item
      */
-    removeById(id: string): boolean;
+    remove(identifier: string, options?: RemoveOptions): Promise<RemoveResult>;
     /**
-     * Find a reference by UUID
+     * Update a reference by citation ID or UUID.
+     * @param identifier - The citation ID or UUID of the reference to update
+     * @param updates - Partial updates to apply to the reference
+     * @param options - Update options (byUuid to use UUID lookup, onIdCollision for collision handling)
+     * @returns Update result with updated item, success status, and any ID changes
      */
-    findByUuid(uuid: string): Reference | undefined;
+    update(identifier: string, updates: Partial<CslItem>, options?: UpdateOptions): Promise<UpdateResult>;
     /**
-     * Find a reference by ID
+     * Find a reference by citation ID or UUID.
+     * @param identifier - The citation ID or UUID of the reference to find
+     * @param options - Find options (byUuid to use UUID lookup)
+     * @returns The CSL item if found, undefined otherwise
      */
-    findById(id: string): Reference | undefined;
+    find(identifier: string, options?: FindOptions): Promise<CslItem | undefined>;
     /**
      * Find a reference by DOI
      */
@@ -51,7 +68,7 @@ export declare class Library {
     /**
      * Get all references
      */
-    getAll(): Reference[];
+    getAll(): Promise<CslItem[]>;
     /**
      * Get the file path
      */
@@ -69,5 +86,31 @@ export declare class Library {
      * Remove reference from all indices and array
      */
     private removeReference;
+    /**
+     * Update a reference with partial updates.
+     * Preserves uuid and created_at, updates timestamp.
+     */
+    private updateReference;
+    /**
+     * Resolve the new ID, handling collisions based on options.
+     */
+    private resolveNewId;
+    /**
+     * Build the updated CslItem, preserving uuid and created_at.
+     */
+    private buildUpdatedItem;
+    /**
+     * Remove a reference from all indices.
+     */
+    private removeFromIndices;
+    /**
+     * Generate an alphabetic suffix for ID collision resolution.
+     * 0 -> 'a', 1 -> 'b', ..., 25 -> 'z', 26 -> 'aa', etc.
+     */
+    private generateSuffix;
+    /**
+     * Resolve ID collision by appending alphabetic suffix.
+     */
+    private resolveIdCollision;
 }
 //# sourceMappingURL=library.d.ts.map

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

@@ -1 +1 @@
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+{"version":3,"file":"library.d.ts","sourceRoot":"","sources":["../../src/core/library.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,kBAAkB,CAAC;AAChD,OAAO,KAAK,EACV,WAAW,EACX,QAAQ,EACR,aAAa,EACb,YAAY,EACZ,aAAa,EACb,YAAY,EACb,MAAM,wBAAwB,CAAC;AAChC,OAAO,EAAE,SAAS,EAAE,MAAM,aAAa,CAAC;AAGxC,YAAY,EAAE,WAAW,EAAE,QAAQ,EAAE,aAAa,EAAE,YAAY,EAAE,MAAM,wBAAwB,CAAC;AAEjG;;;GAGG;AACH,qBAAa,OAAQ,YAAW,QAAQ;IACtC,OAAO,CAAC,QAAQ,CAAS;IACzB,OAAO,CAAC,UAAU,CAAmB;IACrC,OAAO,CAAC,WAAW,CAAuB;IAG1C,OAAO,CAAC,SAAS,CAAqC;IACtD,OAAO,CAAC,OAAO,CAAqC;IACpD,OAAO,CAAC,QAAQ,CAAqC;IACrD,OAAO,CAAC,SAAS,CAAqC;IAEtD,OAAO;IAWP;;OAEG;WACU,IAAI,CAAC,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,OAAO,CAAC;IAQrD;;OAEG;IACG,IAAI,IAAI,OAAO,CAAC,IAAI,CAAC;IAO3B;;;;OAIG;IACG,MAAM,IAAI,OAAO,CAAC,OAAO,CAAC;IA8BhC;;;;OAIG;IACG,GAAG,CAAC,IAAI,EAAE,OAAO,GAAG,OAAO,CAAC,OAAO,CAAC;IAe1C;;;;;OAKG;IACG,MAAM,CAAC,UAAU,EAAE,MAAM,EAAE,OAAO,GAAE,aAAkB,GAAG,OAAO,CAAC,YAAY,CAAC;IAWpF;;;;;;OAMG;IACG,MAAM,CACV,UAAU,EAAE,MAAM,EAClB,OAAO,EAAE,OAAO,CAAC,OAAO,CAAC,EACzB,OAAO,GAAE,aAAkB,GAC1B,OAAO,CAAC,YAAY,CAAC;IAWxB;;;;;OAKG;IACG,IAAI,CAAC,UAAU,EAAE,MAAM,EAAE,OAAO,GAAE,WAAgB,GAAG,OAAO,CAAC,OAAO,GAAG,SAAS,CAAC;IAMvF;;OAEG;IACH,SAAS,CAAC,GAAG,EAAE,MAAM,GAAG,SAAS,GAAG,SAAS;IAI7C;;OAEG;IACH,UAAU,CAAC,IAAI,EAAE,MAAM,GAAG,SAAS,GAAG,SAAS;IAI/C;;OAEG;IACG,MAAM,IAAI,OAAO,CAAC,OAAO,EAAE,CAAC;IAIlC;;OAEG;IACH,WAAW,IAAI,MAAM;IAIrB;;;OAGG;IACH,cAAc,IAAI,MAAM,GAAG,IAAI;IAI/B;;OAEG;IACH,OAAO,CAAC,YAAY;IAoBpB;;OAEG;IACH,OAAO,CAAC,eAAe;IAUvB;;;OAGG;IACH,OAAO,CAAC,eAAe;IAwCvB;;OAEG;IACH,OAAO,CAAC,YAAY;IA0BpB;;OAEG;IACH,OAAO,CAAC,gBAAgB;IAoBxB;;OAEG;IACH,OAAO,CAAC,iBAAiB;IAezB;;;OAGG;IACH,OAAO,CAAC,cAAc;IAatB;;OAEG;IACH,OAAO,CAAC,kBAAkB;CAgB3B"}

package/dist/features/format/bibtex.d.ts

@@ -0,0 +1,6 @@
+import type { CslItem } from "../../core/csl-json/types.js";
+/**
+ * Format references as BibTeX
+ */
+export declare function formatBibtex(items: CslItem[]): string;
+//# sourceMappingURL=bibtex.d.ts.map

package/dist/features/format/bibtex.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"bibtex.d.ts","sourceRoot":"","sources":["../../../src/features/format/bibtex.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,8BAA8B,CAAC;AA+J5D;;GAEG;AACH,wBAAgB,YAAY,CAAC,KAAK,EAAE,OAAO,EAAE,GAAG,MAAM,CAMrD"}

package/dist/features/format/citation-csl.d.ts

@@ -0,0 +1,41 @@
+import "@citation-js/plugin-csl";
+import type { CslItem } from "../../core/csl-json/types.js";
+/**
+ * Options for CSL citation formatting
+ */
+export type CitationFormatOptions = {
+    /**
+     * CSL style name (e.g., 'apa', 'vancouver', 'chicago')
+     * @default 'apa'
+     */
+    style?: string;
+    /**
+     * Output format: text, html, or rtf
+     * @default 'text'
+     */
+    format?: "text" | "html" | "rtf";
+    /**
+     * Locale code (e.g., 'en-US', 'en-GB')
+     * @default 'en-US'
+     */
+    locale?: string;
+};
+/**
+ * Format CSL-JSON items as bibliography using CSL processor.
+ * Falls back to simplified format if CSL processing fails.
+ *
+ * @param items - Array of CSL-JSON items
+ * @param options - Formatting options
+ * @returns Formatted bibliography entries
+ */
+export declare function formatBibliographyCSL(items: CslItem[], options: CitationFormatOptions): string;
+/**
+ * Format CSL-JSON items as in-text citations using CSL processor.
+ * Falls back to simplified format if CSL processing fails.
+ *
+ * @param items - Array of CSL-JSON items
+ * @param options - Formatting options
+ * @returns Formatted in-text citation(s)
+ */
+export declare function formatInTextCSL(items: CslItem[], options: CitationFormatOptions): string;
+//# sourceMappingURL=citation-csl.d.ts.map

package/dist/features/format/citation-csl.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"citation-csl.d.ts","sourceRoot":"","sources":["../../../src/features/format/citation-csl.ts"],"names":[],"mappings":"AACA,OAAO,yBAAyB,CAAC;AACjC,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,8BAA8B,CAAC;AAG5D;;GAEG;AACH,MAAM,MAAM,qBAAqB,GAAG;IAClC;;;OAGG;IACH,KAAK,CAAC,EAAE,MAAM,CAAC;IAEf;;;OAGG;IACH,MAAM,CAAC,EAAE,MAAM,GAAG,MAAM,GAAG,KAAK,CAAC;IAEjC;;;OAGG;IACH,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB,CAAC;AAEF;;;;;;;GAOG;AACH,wBAAgB,qBAAqB,CAAC,KAAK,EAAE,OAAO,EAAE,EAAE,OAAO,EAAE,qBAAqB,GAAG,MAAM,CA+B9F;AAED;;;;;;;GAOG;AACH,wBAAgB,eAAe,CAAC,KAAK,EAAE,OAAO,EAAE,EAAE,OAAO,EAAE,qBAAqB,GAAG,MAAM,CA+BxF"}

package/dist/features/format/citation-fallback.d.ts

@@ -0,0 +1,24 @@
+import type { CslItem } from "../../core/csl-json/types.js";
+/**
+ * Format CSL-JSON items as simplified AMA-like bibliography entries.
+ *
+ * Format: FirstAuthor [et al]. JournalAbbrev. YYYY;volume(issue):pages. PMID:xxxxx [or DOI:xxxxx]. Title.
+ *
+ * Multiple items are separated by double newlines.
+ *
+ * @param items - Array of CSL-JSON items
+ * @returns Formatted bibliography entries separated by double newlines
+ */
+export declare function formatBibliography(items: CslItem[]): string;
+/**
+ * Format CSL-JSON items as simplified in-text citations.
+ *
+ * Format: (FirstAuthor et al, YYYY)
+ *
+ * Multiple items are separated by semicolons and enclosed in parentheses.
+ *
+ * @param items - Array of CSL-JSON items
+ * @returns Formatted in-text citation(s) enclosed in parentheses
+ */
+export declare function formatInText(items: CslItem[]): string;
+//# sourceMappingURL=citation-fallback.d.ts.map

package/dist/features/format/citation-fallback.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"citation-fallback.d.ts","sourceRoot":"","sources":["../../../src/features/format/citation-fallback.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,8BAA8B,CAAC;AAwK5D;;;;;;;;;GASG;AACH,wBAAgB,kBAAkB,CAAC,KAAK,EAAE,OAAO,EAAE,GAAG,MAAM,CAM3D;AAED;;;;;;;;;GASG;AACH,wBAAgB,YAAY,CAAC,KAAK,EAAE,OAAO,EAAE,GAAG,MAAM,CAOrD"}

package/dist/features/format/index.d.ts

@@ -0,0 +1,10 @@
+/**
+ * Output formatters for reference data
+ */
+export { formatJson } from "./json.js";
+export { formatPretty } from "./pretty.js";
+export { formatBibtex } from "./bibtex.js";
+export { formatBibliography, formatInText } from "./citation-fallback.js";
+export { formatBibliographyCSL, formatInTextCSL } from "./citation-csl.js";
+export type { CitationFormatOptions } from "./citation-csl.js";
+//# sourceMappingURL=index.d.ts.map

package/dist/features/format/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/features/format/index.ts"],"names":[],"mappings":"AAAA;;GAEG;AAEH,OAAO,EAAE,UAAU,EAAE,MAAM,WAAW,CAAC;AACvC,OAAO,EAAE,YAAY,EAAE,MAAM,aAAa,CAAC;AAC3C,OAAO,EAAE,YAAY,EAAE,MAAM,aAAa,CAAC;AAC3C,OAAO,EAAE,kBAAkB,EAAE,YAAY,EAAE,MAAM,wBAAwB,CAAC;AAC1E,OAAO,EAAE,qBAAqB,EAAE,eAAe,EAAE,MAAM,mBAAmB,CAAC;AAC3E,YAAY,EAAE,qBAAqB,EAAE,MAAM,mBAAmB,CAAC"}

package/dist/features/format/json.d.ts

@@ -0,0 +1,6 @@
+import type { CslItem } from "../../core/csl-json/types.js";
+/**
+ * Format references as compact JSON
+ */
+export declare function formatJson(items: CslItem[]): string;
+//# sourceMappingURL=json.d.ts.map

package/dist/features/format/json.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"json.d.ts","sourceRoot":"","sources":["../../../src/features/format/json.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,8BAA8B,CAAC;AAE5D;;GAEG;AACH,wBAAgB,UAAU,CAAC,KAAK,EAAE,OAAO,EAAE,GAAG,MAAM,CAEnD"}