@ncukondo/reference-manager 0.1.0 → 0.3.0

package/dist/cli/commands/add.d.ts

@@ -1,22 +1,50 @@
-import type { CslItem } from "../../core/csl-json/types.js";
-import type { DuplicateMatch } from "../../features/duplicate/types.js";
-export interface AddOptions {
+import type { PubmedConfig } from "../../features/import/fetcher.js";
+import { type AddReferencesResult, type AddedItem, type FailedItem, type SkippedItem } from "../../features/operations/add.js";
+import type { ExecutionContext } from "../execution-context.js";
+/**
+ * Options for the add command.
+ */
+export interface AddCommandOptions {
+    /** Input strings (file paths, PMIDs, DOIs) */
+    inputs: string[];
+    /** Skip duplicate detection */
     force: boolean;
+    /** Explicit input format */
+    format?: string;
+    /** PubMed API configuration */
+    pubmedConfig?: PubmedConfig;
+    /** Show verbose error output */
+    verbose?: boolean;
+    /** Content from stdin */
+    stdinContent?: string;
 }
-export interface AddResult {
-    added: boolean;
-    item: CslItem;
-    idChanged: boolean;
-    originalId?: string | undefined;
-    duplicate?: DuplicateMatch | undefined;
-}
 /**
- * Add a new reference to the library.
+ * Result from add command execution.
+ */
+export type AddCommandResult = AddReferencesResult;
+export type { AddedItem, FailedItem, SkippedItem };
+/**
+ * Execute add command.
+ * Routes to server API or direct library operation based on execution context.
+ *
+ * @param options - Add command options
+ * @param context - Execution context (server or local)
+ * @returns Add result containing added, failed, and skipped items
+ */
+export declare function executeAdd(options: AddCommandOptions, context: ExecutionContext): Promise<AddCommandResult>;
+/**
+ * Format add result for CLI output.
+ *
+ * @param result - Add result
+ * @param verbose - Show verbose error output
+ * @returns Formatted output string
+ */
+export declare function formatAddOutput(result: AddCommandResult, verbose: boolean): string;
+/**
+ * Determine exit code based on result.
  *
- * @param existing - Existing library items
- * @param newItem - New item to add
- * @param options - Add options
- * @returns Add result
+ * @param result - Add result
+ * @returns Exit code (0 for success/partial success, 1 for complete failure)
  */
-export declare function add(existing: CslItem[], newItem: CslItem, options: AddOptions): Promise<AddResult>;
+export declare function getExitCode(result: AddCommandResult): number;
 //# sourceMappingURL=add.d.ts.map

package/dist/cli/commands/add.d.ts.map

@@ -1 +1 @@
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package/dist/cli/commands/cite.d.ts

@@ -0,0 +1,49 @@
+import { type CiteResult } from "../../features/operations/cite.js";
+import type { ExecutionContext } from "../execution-context.js";
+/**
+ * Options for the cite command.
+ */
+export interface CiteCommandOptions {
+    identifiers: string[];
+    uuid?: boolean;
+    style?: string;
+    cslFile?: string;
+    locale?: string;
+    format?: "text" | "html" | "rtf";
+    inText?: boolean;
+}
+/**
+ * Result from cite command execution.
+ */
+export type CiteCommandResult = CiteResult;
+/**
+ * Execute cite command.
+ * Routes to server API or direct library operation based on execution context.
+ *
+ * @param options - Cite command options
+ * @param context - Execution context (server or local)
+ * @returns Cite result containing per-identifier results
+ */
+export declare function executeCite(options: CiteCommandOptions, context: ExecutionContext): Promise<CiteCommandResult>;
+/**
+ * Format cite result for CLI output.
+ *
+ * @param result - Cite result
+ * @returns Formatted output string (for stdout)
+ */
+export declare function formatCiteOutput(result: CiteCommandResult): string;
+/**
+ * Format cite errors for stderr.
+ *
+ * @param result - Cite result
+ * @returns Error messages to write to stderr
+ */
+export declare function formatCiteErrors(result: CiteCommandResult): string;
+/**
+ * Determine exit code based on result.
+ *
+ * @param result - Cite result
+ * @returns Exit code (0 for success/partial success, 1 for complete failure)
+ */
+export declare function getCiteExitCode(result: CiteCommandResult): number;
+//# sourceMappingURL=cite.d.ts.map

package/dist/cli/commands/cite.d.ts.map

@@ -0,0 +1 @@
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package/dist/cli/commands/fulltext.d.ts

@@ -0,0 +1,101 @@
+/**
+ * Fulltext CLI commands: attach, get, detach
+ */
+import { type FulltextType } from "../../features/fulltext/index.js";
+import type { ExecutionContext } from "../execution-context.js";
+/**
+ * Options for fulltext attach command
+ */
+export interface FulltextAttachOptions {
+    identifier: string;
+    filePath?: string;
+    type?: FulltextType;
+    move?: boolean;
+    force?: boolean;
+    byUuid?: boolean;
+    fulltextDirectory: string;
+    stdinContent?: Buffer;
+}
+/**
+ * Result from fulltext attach command
+ */
+export interface FulltextAttachResult {
+    success: boolean;
+    filename?: string;
+    type?: FulltextType;
+    overwritten?: boolean;
+    existingFile?: string;
+    requiresConfirmation?: boolean;
+    error?: string;
+}
+/**
+ * Options for fulltext get command
+ */
+export interface FulltextGetOptions {
+    identifier: string;
+    type?: FulltextType;
+    stdout?: boolean;
+    byUuid?: boolean;
+    fulltextDirectory: string;
+}
+/**
+ * Result from fulltext get command
+ */
+export interface FulltextGetResult {
+    success: boolean;
+    paths?: {
+        pdf?: string;
+        markdown?: string;
+    };
+    content?: Buffer;
+    error?: string;
+}
+/**
+ * Options for fulltext detach command
+ */
+export interface FulltextDetachOptions {
+    identifier: string;
+    type?: FulltextType;
+    delete?: boolean;
+    force?: boolean;
+    byUuid?: boolean;
+    fulltextDirectory: string;
+}
+/**
+ * Result from fulltext detach command
+ */
+export interface FulltextDetachResult {
+    success: boolean;
+    detached?: FulltextType[];
+    deleted?: FulltextType[];
+    error?: string;
+}
+/**
+ * Execute fulltext attach command
+ */
+export declare function executeFulltextAttach(options: FulltextAttachOptions, context: ExecutionContext): Promise<FulltextAttachResult>;
+/**
+ * Execute fulltext get command
+ */
+export declare function executeFulltextGet(options: FulltextGetOptions, context: ExecutionContext): Promise<FulltextGetResult>;
+/**
+ * Execute fulltext detach command
+ */
+export declare function executeFulltextDetach(options: FulltextDetachOptions, context: ExecutionContext): Promise<FulltextDetachResult>;
+/**
+ * Format fulltext attach output
+ */
+export declare function formatFulltextAttachOutput(result: FulltextAttachResult): string;
+/**
+ * Format fulltext get output
+ */
+export declare function formatFulltextGetOutput(result: FulltextGetResult): string;
+/**
+ * Format fulltext detach output
+ */
+export declare function formatFulltextDetachOutput(result: FulltextDetachResult): string;
+/**
+ * Get exit code for fulltext command result
+ */
+export declare function getFulltextExitCode(result: FulltextAttachResult | FulltextGetResult | FulltextDetachResult): number;
+//# sourceMappingURL=fulltext.d.ts.map

package/dist/cli/commands/fulltext.d.ts.map

@@ -0,0 +1 @@
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package/dist/cli/commands/index.d.ts

@@ -1,16 +1,20 @@
 /**
  * CLI commands
  */
-export { list } from "./list.js";
-export type { ListOptions } from "./list.js";
-export { search } from "./search.js";
-export type { SearchOptions } from "./search.js";
-export { add } from "./add.js";
-export type { AddOptions, AddResult } from "./add.js";
-export { remove } from "./remove.js";
-export type { RemoveOptions, RemoveResult } from "./remove.js";
-export { update } from "./update.js";
-export type { UpdateOptions, UpdateResult } from "./update.js";
+export { executeList, formatListOutput } from "./list.js";
+export type { ListCommandOptions, ListCommandResult } from "./list.js";
+export { executeSearch, formatSearchOutput } from "./search.js";
+export type { SearchCommandOptions, SearchCommandResult } from "./search.js";
+export { executeAdd, formatAddOutput, getExitCode } from "./add.js";
+export type { AddCommandOptions, AddCommandResult, AddedItem, FailedItem, SkippedItem, } from "./add.js";
+export { executeRemove, formatRemoveOutput } from "./remove.js";
+export type { RemoveCommandOptions, RemoveCommandResult } from "./remove.js";
+export { executeUpdate, formatUpdateOutput } from "./update.js";
+export type { UpdateCommandOptions, UpdateCommandResult } from "./update.js";
 export { serverStart, serverStop, serverStatus } from "./server.js";
 export type { ServerStartOptions, ServerInfo } from "./server.js";
+export { executeCite, formatCiteOutput, formatCiteErrors, getCiteExitCode } from "./cite.js";
+export type { CiteCommandOptions, CiteCommandResult } from "./cite.js";
+export { executeFulltextAttach, executeFulltextGet, executeFulltextDetach, formatFulltextAttachOutput, formatFulltextGetOutput, formatFulltextDetachOutput, getFulltextExitCode, } from "./fulltext.js";
+export type { FulltextAttachOptions, FulltextAttachResult, FulltextGetOptions, FulltextGetResult, FulltextDetachOptions, FulltextDetachResult, } from "./fulltext.js";
 //# sourceMappingURL=index.d.ts.map

package/dist/cli/commands/index.d.ts.map

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package/dist/cli/commands/list.d.ts

@@ -1,15 +1,32 @@
-import type { CslItem } from "../../core/csl-json/types.js";
-export interface ListOptions {
+import { type ListResult } from "../../features/operations/list.js";
+import type { ExecutionContext } from "../execution-context.js";
+/**
+ * Options for the list command.
+ */
+export interface ListCommandOptions {
     json?: boolean;
     idsOnly?: boolean;
     uuid?: boolean;
     bibtex?: boolean;
 }
 /**
- * List all references in the library.
+ * Result from list command execution.
+ */
+export type ListCommandResult = ListResult;
+/**
+ * Execute list command.
+ * Routes to server API or direct library operation based on execution context.
+ *
+ * @param options - List command options
+ * @param context - Execution context (server or local)
+ * @returns List result containing formatted items
+ */
+export declare function executeList(options: ListCommandOptions, context: ExecutionContext): Promise<ListCommandResult>;
+/**
+ * Format list result for CLI output.
  *
- * @param items - Array of CSL items
- * @param options - Output format options
+ * @param result - List result
+ * @returns Formatted output string
  */
-export declare function list(items: CslItem[], options: ListOptions): Promise<void>;
+export declare function formatListOutput(result: ListCommandResult): string;
 //# sourceMappingURL=list.d.ts.map

package/dist/cli/commands/list.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"list.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/list.ts"],"names":[],"mappings":"AAAA,OAAO,EAEL,KAAK,UAAU,EAEhB,MAAM,mCAAmC,CAAC;AAC3C,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAC;AAEhE;;GAEG;AACH,MAAM,WAAW,kBAAkB;IACjC,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,MAAM,CAAC,EAAE,OAAO,CAAC;CAClB;AAED;;GAEG;AACH,MAAM,MAAM,iBAAiB,GAAG,UAAU,CAAC;AA4B3C;;;;;;;GAOG;AACH,wBAAsB,WAAW,CAC/B,OAAO,EAAE,kBAAkB,EAC3B,OAAO,EAAE,gBAAgB,GACxB,OAAO,CAAC,iBAAiB,CAAC,CAW5B;AAED;;;;;GAKG;AACH,wBAAgB,gBAAgB,CAAC,MAAM,EAAE,iBAAiB,GAAG,MAAM,CAKlE"}

package/dist/cli/commands/remove.d.ts

@@ -1,19 +1,54 @@
 import type { CslItem } from "../../core/csl-json/types.js";
-export interface RemoveOptions {
-    byUuid: boolean;
-}
-export interface RemoveResult {
-    removed: boolean;
-    item?: CslItem | undefined;
-    remaining: CslItem[];
+import type { FulltextType } from "../../features/fulltext/index.js";
+import { type RemoveResult } from "../../features/operations/remove.js";
+import type { ExecutionContext } from "../execution-context.js";
+/**
+ * Options for the remove command.
+ */
+export interface RemoveCommandOptions {
+    identifier: string;
+    byUuid?: boolean;
 }
 /**
- * Remove a reference from the library.
+ * Result from remove command execution.
+ */
+export type RemoveCommandResult = RemoveResult;
+/**
+ * Execute remove command.
+ * Routes to server API or direct library operation based on execution context.
  *
- * @param items - Library items
- * @param identifier - Reference ID or UUID
- * @param options - Remove options
+ * @param options - Remove command options
+ * @param context - Execution context (server or local)
  * @returns Remove result
  */
-export declare function remove(items: CslItem[], identifier: string, options: RemoveOptions): Promise<RemoveResult>;
+export declare function executeRemove(options: RemoveCommandOptions, context: ExecutionContext): Promise<RemoveCommandResult>;
+/**
+ * Format remove result for CLI output.
+ *
+ * @param result - Remove result
+ * @param identifier - The identifier that was used
+ * @returns Formatted output string
+ */
+export declare function formatRemoveOutput(result: RemoveCommandResult, identifier: string): string;
+/**
+ * Get fulltext attachment types from a CSL item.
+ *
+ * @param item - CSL item to check
+ * @returns Array of attached fulltext types
+ */
+export declare function getFulltextAttachmentTypes(item: CslItem): FulltextType[];
+/**
+ * Format fulltext warning message for remove confirmation.
+ *
+ * @param types - Attached fulltext types
+ * @returns Warning message string
+ */
+export declare function formatFulltextWarning(types: FulltextType[]): string;
+/**
+ * Delete fulltext files associated with a CSL item.
+ *
+ * @param item - CSL item with fulltext attachments
+ * @param fulltextDirectory - Directory containing fulltext files
+ */
+export declare function deleteFulltextFiles(item: CslItem, fulltextDirectory: string): Promise<void>;
 //# sourceMappingURL=remove.d.ts.map

package/dist/cli/commands/remove.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"remove.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/remove.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,8BAA8B,CAAC;AAC5D,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,kCAAkC,CAAC;AACrE,OAAO,EAAE,KAAK,YAAY,EAAmB,MAAM,qCAAqC,CAAC;AACzF,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAC;AAEhE;;GAEG;AACH,MAAM,WAAW,oBAAoB;IACnC,UAAU,EAAE,MAAM,CAAC;IACnB,MAAM,CAAC,EAAE,OAAO,CAAC;CAClB;AAED;;GAEG;AACH,MAAM,MAAM,mBAAmB,GAAG,YAAY,CAAC;AAE/C;;;;;;;GAOG;AACH,wBAAsB,aAAa,CACjC,OAAO,EAAE,oBAAoB,EAC7B,OAAO,EAAE,gBAAgB,GACxB,OAAO,CAAC,mBAAmB,CAAC,CAU9B;AAED;;;;;;GAMG;AACH,wBAAgB,kBAAkB,CAAC,MAAM,EAAE,mBAAmB,EAAE,UAAU,EAAE,MAAM,GAAG,MAAM,CAW1F;AAED;;;;;GAKG;AACH,wBAAgB,0BAA0B,CAAC,IAAI,EAAE,OAAO,GAAG,YAAY,EAAE,CAYxE;AAED;;;;;GAKG;AACH,wBAAgB,qBAAqB,CAAC,KAAK,EAAE,YAAY,EAAE,GAAG,MAAM,CAInE;AAED;;;;;GAKG;AACH,wBAAsB,mBAAmB,CAAC,IAAI,EAAE,OAAO,EAAE,iBAAiB,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CAsBjG"}

package/dist/cli/commands/search.d.ts

@@ -1,16 +1,33 @@
-import type { CslItem } from "../../core/csl-json/types.js";
-export interface SearchOptions {
+import { type SearchResult } from "../../features/operations/search.js";
+import type { ExecutionContext } from "../execution-context.js";
+/**
+ * Options for the search command.
+ */
+export interface SearchCommandOptions {
+    query: string;
     json?: boolean;
     idsOnly?: boolean;
     uuid?: boolean;
     bibtex?: boolean;
 }
 /**
- * Search references in the library.
+ * Result from search command execution.
+ */
+export type SearchCommandResult = SearchResult;
+/**
+ * Execute search command.
+ * Routes to server API or direct library operation based on execution context.
+ *
+ * @param options - Search command options
+ * @param context - Execution context (server or local)
+ * @returns Search result containing formatted items
+ */
+export declare function executeSearch(options: SearchCommandOptions, context: ExecutionContext): Promise<SearchCommandResult>;
+/**
+ * Format search result for CLI output.
  *
- * @param items - Array of CSL items
- * @param query - Search query string
- * @param options - Output format options
+ * @param result - Search result
+ * @returns Formatted output string
  */
-export declare function search(items: CslItem[], query: string, options: SearchOptions): Promise<void>;
+export declare function formatSearchOutput(result: SearchCommandResult): string;
 //# sourceMappingURL=search.d.ts.map

package/dist/cli/commands/search.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"search.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/search.ts"],"names":[],"mappings":"AAAA,OAAO,EAEL,KAAK,YAAY,EAElB,MAAM,qCAAqC,CAAC;AAC7C,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAC;AAEhE;;GAEG;AACH,MAAM,WAAW,oBAAoB;IACnC,KAAK,EAAE,MAAM,CAAC;IACd,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,MAAM,CAAC,EAAE,OAAO,CAAC;CAClB;AAED;;GAEG;AACH,MAAM,MAAM,mBAAmB,GAAG,YAAY,CAAC;AA4B/C;;;;;;;GAOG;AACH,wBAAsB,aAAa,CACjC,OAAO,EAAE,oBAAoB,EAC7B,OAAO,EAAE,gBAAgB,GACxB,OAAO,CAAC,mBAAmB,CAAC,CAW9B;AAED;;;;;GAKG;AACH,wBAAgB,kBAAkB,CAAC,MAAM,EAAE,mBAAmB,GAAG,MAAM,CAKtE"}

package/dist/cli/commands/update.d.ts

@@ -1,20 +1,33 @@
 import type { CslItem } from "../../core/csl-json/types.js";
-export interface UpdateOptions {
-    byUuid: boolean;
-}
-export interface UpdateResult {
-    updated: boolean;
-    item?: CslItem | undefined;
-    items: CslItem[];
+import { type UpdateOperationResult } from "../../features/operations/update.js";
+import type { ExecutionContext } from "../execution-context.js";
+/**
+ * Options for the update command.
+ */
+export interface UpdateCommandOptions {
+    identifier: string;
+    updates: Partial<CslItem>;
+    byUuid?: boolean;
 }
 /**
- * Update a reference in the library.
+ * Result from update command execution.
+ */
+export type UpdateCommandResult = UpdateOperationResult;
+/**
+ * Execute update command.
+ * Routes to server API or direct library operation based on execution context.
  *
- * @param items - Library items
- * @param identifier - Reference ID or UUID
- * @param updates - Partial updates to apply
- * @param options - Update options
+ * @param options - Update command options
+ * @param context - Execution context (server or local)
  * @returns Update result
  */
-export declare function update(items: CslItem[], identifier: string, updates: Partial<CslItem>, options: UpdateOptions): Promise<UpdateResult>;
+export declare function executeUpdate(options: UpdateCommandOptions, context: ExecutionContext): Promise<UpdateCommandResult>;
+/**
+ * Format update result for CLI output.
+ *
+ * @param result - Update result
+ * @param identifier - The identifier that was used
+ * @returns Formatted output string
+ */
+export declare function formatUpdateOutput(result: UpdateCommandResult, identifier: string): string;
 //# sourceMappingURL=update.d.ts.map

package/dist/cli/commands/update.d.ts.map

@@ -1 +1 @@
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package/dist/cli/execution-context.d.ts

@@ -0,0 +1,60 @@
+/**
+ * Execution Context for CLI Commands
+ *
+ * Provides a discriminated union type to distinguish between server and local execution modes.
+ * This enables CLI commands to avoid redundant library loading when a server is available.
+ */
+import type { Config } from "../config/schema.js";
+import type { Library } from "../core/library.js";
+import { ServerClient } from "./server-client.js";
+/**
+ * Server execution context - uses ServerClient for operations
+ */
+export interface ServerExecutionContext {
+    type: "server";
+    client: ServerClient;
+}
+/**
+ * Local execution context - uses Library directly
+ */
+export interface LocalExecutionContext {
+    type: "local";
+    library: Library;
+}
+/**
+ * Discriminated union type for execution context.
+ * Commands can use this to determine whether to use server or local operations.
+ *
+ * @example
+ * ```typescript
+ * if (context.type === "server") {
+ *   // Use context.client for server operations
+ *   const result = await context.client.list(options);
+ * } else {
+ *   // Use context.library for local operations
+ *   const items = context.library.getAll();
+ * }
+ * ```
+ */
+export type ExecutionContext = ServerExecutionContext | LocalExecutionContext;
+/**
+ * Creates an execution context based on the current configuration.
+ *
+ * This function checks for an available server connection first.
+ * If a server is available, it returns a server context to avoid loading the library.
+ * Otherwise, it loads the library and returns a local context.
+ *
+ * @param config - The application configuration
+ * @param loadLibrary - Function to load the library (injected for testability)
+ * @returns Promise resolving to either a server or local execution context
+ */
+export declare function createExecutionContext(config: Config, loadLibrary: (path: string) => Promise<Library>): Promise<ExecutionContext>;
+/**
+ * Type guard to check if context is a server context
+ */
+export declare function isServerContext(context: ExecutionContext): context is ServerExecutionContext;
+/**
+ * Type guard to check if context is a local context
+ */
+export declare function isLocalContext(context: ExecutionContext): context is LocalExecutionContext;
+//# sourceMappingURL=execution-context.d.ts.map

package/dist/cli/execution-context.d.ts.map

@@ -0,0 +1 @@
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package/dist/cli/helpers.d.ts

@@ -58,4 +58,22 @@ export declare function isTTY(): boolean;
  * @returns True if user confirmed (y/yes), false otherwise
  */
 export declare function readConfirmation(prompt: string): Promise<boolean>;
+/**
+ * Read stdin content and split into inputs.
+ * Used for reading identifiers from stdin.
+ * @returns Array of input strings (split by whitespace)
+ */
+export declare function readStdinInputs(): Promise<string[]>;
+/**
+ * Read raw stdin content without splitting.
+ * Used for reading file content (JSON, BibTeX, RIS) from stdin.
+ * @returns Raw stdin content as string
+ */
+export declare function readStdinContent(): Promise<string>;
+/**
+ * Read raw stdin content as Buffer.
+ * Used for reading binary file content (PDF) from stdin.
+ * @returns Raw stdin content as Buffer
+ */
+export declare function readStdinBuffer(): Promise<Buffer>;
 //# sourceMappingURL=helpers.d.ts.map

package/dist/cli/helpers.d.ts.map

@@ -1 +1 @@
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package/dist/cli/index.d.ts.map

@@ -1 +1 @@
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