@ncukondo/reference-manager 0.1.0 → 0.3.0

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,MAgC3B,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;AA+ID;;;;;;;;;GASG;AACH,wBAAgB,UAAU,CAAC,OAAO,GAAE,iBAAsB,GAAG,MAAM,CAwClE"}

package/dist/config/schema.d.ts

@@ -35,6 +35,40 @@ 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
  */
@@ -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.$strip>;
 /**
  * Partial configuration schema (for TOML files)
@@ -102,6 +153,32 @@ export declare const partialConfigSchema: z.ZodObject<{
         autoStopMinutes: z.ZodOptional<z.ZodNumber>;
         auto_stop_minutes: z.ZodOptional<z.ZodNumber>;
     }, z.core.$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 +187,10 @@ 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 +202,9 @@ 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 @@
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+{"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,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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;iBA4DhB,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;AAyKF;;GAEG;AACH,wBAAgB,sBAAsB,CAAC,OAAO,EAAE,aAAa,GAAG,iBAAiB,CAmEhF"}

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

@@ -4,7 +4,11 @@ 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>>;
+}, z.core.$loose>;
 export declare const CslItemSchema: z.ZodObject<{
     id: z.ZodString;
     type: z.ZodString;
@@ -59,7 +63,11 @@ export declare const CslItemSchema: z.ZodObject<{
         created_at: z.ZodString;
         timestamp: z.ZodString;
         additional_urls: z.ZodOptional<z.ZodArray<z.ZodString>>;
-    }, z.core.$strip>>;
+        fulltext: z.ZodOptional<z.ZodObject<{
+            pdf: z.ZodOptional<z.ZodString>;
+            markdown: z.ZodOptional<z.ZodString>;
+        }, z.core.$strip>>;
+    }, z.core.$loose>>;
 }, z.core.$loose>;
 export declare const CslLibrarySchema: z.ZodArray<z.ZodObject<{
     id: z.ZodString;
@@ -115,7 +123,11 @@ export declare const CslLibrarySchema: z.ZodArray<z.ZodObject<{
         created_at: z.ZodString;
         timestamp: z.ZodString;
         additional_urls: z.ZodOptional<z.ZodArray<z.ZodString>>;
-    }, z.core.$strip>>;
+        fulltext: z.ZodOptional<z.ZodObject<{
+            pdf: z.ZodOptional<z.ZodString>;
+            markdown: z.ZodOptional<z.ZodString>;
+        }, z.core.$strip>>;
+    }, z.core.$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;;;;;;;;;iBAQL,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.d.ts

@@ -1,5 +1,25 @@
 import type { CslItem } from "./csl-json/types";
 import { Reference } from "./reference";
+/**
+ * Options for update operations
+ */
+export interface UpdateOptions {
+    /** How to handle ID collision: 'fail' (default) or 'suffix' */
+    onIdCollision?: "fail" | "suffix";
+}
+/**
+ * Result of an update operation
+ */
+export interface UpdateResult {
+    /** Whether the update was successful */
+    updated: boolean;
+    /** 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;
+}
 /**
  * Library manager for CSL-JSON references
  */
@@ -32,6 +52,20 @@ export declare class Library {
      * Remove a reference by ID
      */
     removeById(id: string): boolean;
+    /**
+     * Update a reference by UUID.
+     * @param uuid - The UUID of the reference to update
+     * @param updates - Partial updates to apply to the reference
+     * @returns true if the reference was found and updated, false otherwise
+     */
+    updateByUuid(uuid: string, updates: Partial<CslItem>, options?: UpdateOptions): UpdateResult;
+    /**
+     * Update a reference by ID.
+     * @param id - The ID of the reference to update
+     * @param updates - Partial updates to apply to the reference
+     * @returns true if the reference was found and updated, false otherwise
+     */
+    updateById(id: string, updates: Partial<CslItem>, options?: UpdateOptions): UpdateResult;
     /**
      * Find a reference by UUID
      */
@@ -69,5 +103,31 @@ 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,EAAE,SAAS,EAAE,MAAM,aAAa,CAAC;AAExC;;GAEG;AACH,MAAM,WAAW,aAAa;IAC5B,+DAA+D;IAC/D,aAAa,CAAC,EAAE,MAAM,GAAG,QAAQ,CAAC;CACnC;AAED;;GAEG;AACH,MAAM,WAAW,YAAY;IAC3B,wCAAwC;IACxC,OAAO,EAAE,OAAO,CAAC;IACjB,uFAAuF;IACvF,WAAW,CAAC,EAAE,OAAO,CAAC;IACtB,6DAA6D;IAC7D,SAAS,CAAC,EAAE,OAAO,CAAC;IACpB,uEAAuE;IACvE,KAAK,CAAC,EAAE,MAAM,CAAC;CAChB;AAED;;GAEG;AACH,qBAAa,OAAO;IAClB,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;;OAEG;IACH,GAAG,CAAC,IAAI,EAAE,OAAO,GAAG,IAAI;IAYxB;;OAEG;IACH,YAAY,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO;IASnC;;OAEG;IACH,UAAU,CAAC,EAAE,EAAE,MAAM,GAAG,OAAO;IAS/B;;;;;OAKG;IACH,YAAY,CAAC,IAAI,EAAE,MAAM,EAAE,OAAO,EAAE,OAAO,CAAC,OAAO,CAAC,EAAE,OAAO,GAAE,aAAkB,GAAG,YAAY;IAShG;;;;;OAKG;IACH,UAAU,CAAC,EAAE,EAAE,MAAM,EAAE,OAAO,EAAE,OAAO,CAAC,OAAO,CAAC,EAAE,OAAO,GAAE,aAAkB,GAAG,YAAY;IAS5F;;OAEG;IACH,UAAU,CAAC,IAAI,EAAE,MAAM,GAAG,SAAS,GAAG,SAAS;IAI/C;;OAEG;IACH,QAAQ,CAAC,EAAE,EAAE,MAAM,GAAG,SAAS,GAAG,SAAS;IAI3C;;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;IACH,MAAM,IAAI,SAAS,EAAE;IAIrB;;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"}

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

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

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

@@ -0,0 +1 @@
+{"version":3,"file":"pretty.d.ts","sourceRoot":"","sources":["../../../src/features/format/pretty.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,8BAA8B,CAAC;AA+E5D;;GAEG;AACH,wBAAgB,YAAY,CAAC,KAAK,EAAE,OAAO,EAAE,GAAG,MAAM,CAMrD"}

package/dist/features/fulltext/filename.d.ts

@@ -0,0 +1,17 @@
+/**
+ * Fulltext filename generation
+ */
+import type { CslItem } from "../../core/csl-json/types.js";
+import { type FulltextType } from "./types.js";
+/**
+ * Generate a filename for a fulltext file.
+ *
+ * Format: {id}[-PMID{PMID}]-{uuid}.{ext}
+ *
+ * @param item - CSL item to generate filename for
+ * @param type - Fulltext type (pdf or markdown)
+ * @returns Generated filename
+ * @throws Error if custom.uuid is missing
+ */
+export declare function generateFulltextFilename(item: CslItem, type: FulltextType): string;
+//# sourceMappingURL=filename.d.ts.map

package/dist/features/fulltext/filename.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"filename.d.ts","sourceRoot":"","sources":["../../../src/features/fulltext/filename.ts"],"names":[],"mappings":"AAAA;;GAEG;AAEH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,8BAA8B,CAAC;AAC5D,OAAO,EAAuB,KAAK,YAAY,EAAE,MAAM,YAAY,CAAC;AAEpE;;;;;;;;;GASG;AACH,wBAAgB,wBAAwB,CAAC,IAAI,EAAE,OAAO,EAAE,IAAI,EAAE,YAAY,GAAG,MAAM,CAkBlF"}

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

@@ -0,0 +1,7 @@
+/**
+ * Fulltext management exports
+ */
+export * from "./types.js";
+export { generateFulltextFilename } from "./filename.js";
+export { FulltextManager, FulltextIOError, FulltextNotAttachedError, type AttachOptions, type AttachResult, type DetachOptions, type DetachResult, } from "./manager.js";
+//# sourceMappingURL=index.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/features/fulltext/index.ts"],"names":[],"mappings":"AAAA;;GAEG;AAEH,cAAc,YAAY,CAAC;AAC3B,OAAO,EAAE,wBAAwB,EAAE,MAAM,eAAe,CAAC;AACzD,OAAO,EACL,eAAe,EACf,eAAe,EACf,wBAAwB,EACxB,KAAK,aAAa,EAClB,KAAK,YAAY,EACjB,KAAK,aAAa,EAClB,KAAK,YAAY,GAClB,MAAM,cAAc,CAAC"}

package/dist/features/fulltext/manager.d.ts

@@ -0,0 +1,109 @@
+/**
+ * Fulltext file management
+ */
+import type { CslItem } from "../../core/csl-json/types.js";
+import type { FulltextType } from "./types.js";
+/**
+ * Error thrown when fulltext I/O operation fails
+ */
+export declare class FulltextIOError extends Error {
+    readonly cause?: Error | undefined;
+    constructor(message: string, cause?: Error | undefined);
+}
+/**
+ * Error thrown when trying to detach non-attached fulltext
+ */
+export declare class FulltextNotAttachedError extends Error {
+    readonly itemId: string;
+    readonly type: FulltextType;
+    constructor(itemId: string, type: FulltextType);
+}
+/**
+ * Options for attachFile
+ */
+export interface AttachOptions {
+    /** Move file instead of copy (default: false) */
+    move?: boolean;
+    /** Overwrite existing attachment without confirmation (default: false) */
+    force?: boolean;
+}
+/**
+ * Result of attachFile operation
+ */
+export interface AttachResult {
+    /** Generated filename */
+    filename: string;
+    /** Existing filename if already attached (when force=false) */
+    existingFile?: string;
+    /** Whether existing file was overwritten */
+    overwritten: boolean;
+    /** Old filename that was deleted (when force=true and filename changed) */
+    deletedOldFile?: string;
+}
+/**
+ * Options for detachFile
+ */
+export interface DetachOptions {
+    /** Delete file from disk (default: false, metadata-only detach) */
+    delete?: boolean;
+}
+/**
+ * Result of detachFile operation
+ */
+export interface DetachResult {
+    /** Detached filename */
+    filename: string;
+    /** Whether file was deleted from disk */
+    deleted: boolean;
+}
+/**
+ * Manages fulltext file operations
+ */
+export declare class FulltextManager {
+    private readonly fulltextDirectory;
+    constructor(fulltextDirectory: string);
+    /**
+     * Ensure the fulltext directory exists
+     */
+    ensureDirectory(): Promise<void>;
+    /**
+     * Attach a file to a reference
+     */
+    attachFile(item: CslItem, sourcePath: string, type: FulltextType, options?: AttachOptions): Promise<AttachResult>;
+    /**
+     * Validate that source file exists
+     */
+    private validateSourceFile;
+    /**
+     * Delete old file if force mode and filename changed
+     * @returns Deleted filename or undefined
+     */
+    private deleteOldFileIfNeeded;
+    /**
+     * Copy or move file to destination
+     */
+    private copyOrMoveFile;
+    /**
+     * Get the full path for an attached file
+     * @returns Full path or null if not attached
+     */
+    getFilePath(item: CslItem, type: FulltextType): string | null;
+    /**
+     * Detach a file from a reference
+     */
+    detachFile(item: CslItem, type: FulltextType, options?: DetachOptions): Promise<DetachResult>;
+    /**
+     * Get list of attached fulltext types
+     */
+    getAttachedTypes(item: CslItem): FulltextType[];
+    /**
+     * Check if item has attachment
+     * @param type Optional type to check; if omitted, checks for any attachment
+     */
+    hasAttachment(item: CslItem, type?: FulltextType): boolean;
+    /**
+     * Get existing filename from item metadata
+     */
+    private getExistingFilename;
+}
+//# sourceMappingURL=manager.d.ts.map

package/dist/features/fulltext/manager.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"manager.d.ts","sourceRoot":"","sources":["../../../src/features/fulltext/manager.ts"],"names":[],"mappings":"AAAA;;GAEG;AAKH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,8BAA8B,CAAC;AAE5D,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,YAAY,CAAC;AAE/C;;GAEG;AACH,qBAAa,eAAgB,SAAQ,KAAK;aAGtB,KAAK,CAAC,EAAE,KAAK;gBAD7B,OAAO,EAAE,MAAM,EACC,KAAK,CAAC,EAAE,KAAK,YAAA;CAKhC;AAED;;GAEG;AACH,qBAAa,wBAAyB,SAAQ,KAAK;aAE/B,MAAM,EAAE,MAAM;aACd,IAAI,EAAE,YAAY;gBADlB,MAAM,EAAE,MAAM,EACd,IAAI,EAAE,YAAY;CAKrC;AAED;;GAEG;AACH,MAAM,WAAW,aAAa;IAC5B,iDAAiD;IACjD,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,0EAA0E;IAC1E,KAAK,CAAC,EAAE,OAAO,CAAC;CACjB;AAED;;GAEG;AACH,MAAM,WAAW,YAAY;IAC3B,yBAAyB;IACzB,QAAQ,EAAE,MAAM,CAAC;IACjB,+DAA+D;IAC/D,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,4CAA4C;IAC5C,WAAW,EAAE,OAAO,CAAC;IACrB,2EAA2E;IAC3E,cAAc,CAAC,EAAE,MAAM,CAAC;CACzB;AAED;;GAEG;AACH,MAAM,WAAW,aAAa;IAC5B,mEAAmE;IACnE,MAAM,CAAC,EAAE,OAAO,CAAC;CAClB;AAED;;GAEG;AACH,MAAM,WAAW,YAAY;IAC3B,wBAAwB;IACxB,QAAQ,EAAE,MAAM,CAAC;IACjB,yCAAyC;IACzC,OAAO,EAAE,OAAO,CAAC;CAClB;AAED;;GAEG;AACH,qBAAa,eAAe;IACd,OAAO,CAAC,QAAQ,CAAC,iBAAiB;gBAAjB,iBAAiB,EAAE,MAAM;IAEtD;;OAEG;IACG,eAAe,IAAI,OAAO,CAAC,IAAI,CAAC;IAItC;;OAEG;IACG,UAAU,CACd,IAAI,EAAE,OAAO,EACb,UAAU,EAAE,MAAM,EAClB,IAAI,EAAE,YAAY,EAClB,OAAO,CAAC,EAAE,aAAa,GACtB,OAAO,CAAC,YAAY,CAAC;IAyCxB;;OAEG;IACH,OAAO,CAAC,kBAAkB;IAM1B;;;OAGG;YACW,qBAAqB;IAkBnC;;OAEG;YACW,cAAc;IAgB5B;;;OAGG;IACH,WAAW,CAAC,IAAI,EAAE,OAAO,EAAE,IAAI,EAAE,YAAY,GAAG,MAAM,GAAG,IAAI;IAQ7D;;OAEG;IACG,UAAU,CACd,IAAI,EAAE,OAAO,EACb,IAAI,EAAE,YAAY,EAClB,OAAO,CAAC,EAAE,aAAa,GACtB,OAAO,CAAC,YAAY,CAAC;IAuBxB;;OAEG;IACH,gBAAgB,CAAC,IAAI,EAAE,OAAO,GAAG,YAAY,EAAE;IAc/C;;;OAGG;IACH,aAAa,CAAC,IAAI,EAAE,OAAO,EAAE,IAAI,CAAC,EAAE,YAAY,GAAG,OAAO;IAO1D;;OAEG;IACH,OAAO,CAAC,mBAAmB;CAO5B"}

package/dist/features/fulltext/types.d.ts

@@ -0,0 +1,12 @@
+/**
+ * Fulltext management types
+ */
+/**
+ * Supported fulltext file types
+ */
+export type FulltextType = "pdf" | "markdown";
+/**
+ * File extensions for each fulltext type
+ */
+export declare const FULLTEXT_EXTENSIONS: Record<FulltextType, string>;
+//# sourceMappingURL=types.d.ts.map

package/dist/features/fulltext/types.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"types.d.ts","sourceRoot":"","sources":["../../../src/features/fulltext/types.ts"],"names":[],"mappings":"AAAA;;GAEG;AAEH;;GAEG;AACH,MAAM,MAAM,YAAY,GAAG,KAAK,GAAG,UAAU,CAAC;AAE9C;;GAEG;AACH,eAAO,MAAM,mBAAmB,EAAE,MAAM,CAAC,YAAY,EAAE,MAAM,CAG5D,CAAC"}

package/dist/features/import/cache.d.ts

@@ -0,0 +1,37 @@
+/**
+ * Response cache for PMID and DOI metadata
+ *
+ * In-memory cache with TTL to avoid redundant API calls.
+ * - Per ADR-001: No persistent cache files on disk
+ * - Cache is warm during interactive sessions (server mode)
+ * - CLI invocations start fresh
+ */
+import type { CslItem } from "../../core/csl-json/types.js";
+/**
+ * Cache configuration
+ */
+export interface CacheConfig {
+    /** Time-to-live in milliseconds (default: 1 hour) */
+    ttlMs?: number;
+}
+/**
+ * Get cached PMID result
+ */
+export declare function getPmidFromCache(pmid: string): CslItem | undefined;
+/**
+ * Cache PMID result
+ */
+export declare function cachePmidResult(pmid: string, item: CslItem, config?: CacheConfig): void;
+/**
+ * Get cached DOI result
+ */
+export declare function getDoiFromCache(doi: string): CslItem | undefined;
+/**
+ * Cache DOI result
+ */
+export declare function cacheDoiResult(doi: string, item: CslItem, config?: CacheConfig): void;
+/**
+ * Reset all caches (for test isolation)
+ */
+export declare function resetCache(): void;
+//# sourceMappingURL=cache.d.ts.map

package/dist/features/import/cache.d.ts.map

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