@alextis59/athena 1.0.0

package/LICENSE

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+ISC License
+
+Copyright (c) 2026 Athena contributors
+
+Permission to use, copy, modify, and/or distribute this software for any
+purpose with or without fee is hereby granted, provided that the above
+copyright notice and this permission notice appear in all copies.
+
+THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH
+REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND
+FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT,
+INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM
+LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR
+OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR
+PERFORMANCE OF THIS SOFTWARE.

package/README.md

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+# Athena
+
+Athena is a local-first documentation RAG command for project folders. It
+indexes Markdown, MDX, text, RST, AsciiDoc, HTML, extensionless documentation,
+and PDFs into a local `.athena/index.sqlite` cache, then exposes search, source
+reading, cited terminal answers, a local web UI, and an optional read-only MCP
+bridge for external coding agents.
+
+The installed command is `athena`. The npm package is published as
+`@alextis59/athena` because the unscoped `athena` package name is already taken
+on npm.
+
+## Install
+
+```bash
+npm install -g @alextis59/athena
+```
+
+For ad hoc use inside a documentation folder:
+
+```bash
+npx @alextis59/athena
+```
+
+For development from this checkout:
+
+```bash
+npm install
+npm run build
+npm link
+athena --help
+```
+
+## Commands
+
+```bash
+athena                 # build or update the local index, then start the UI
+athena index           # build or update .athena/index.sqlite only
+athena serve           # serve an existing index
+athena serve --build   # build first, then serve
+athena ask "..."       # one-shot terminal answer with citations
+athena doctor          # inspect config, index, parser, embedding, and port state
+athena mcp             # stdio MCP server for external coding agents
+```
+
+Common options:
+
+```bash
+--root <path>      Project root to inspect
+--config <path>    Explicit athena.config.ts, .mjs, or .json file
+--db <path>        SQLite index path
+--host <host>      Server bind host
+--port <port>      Server port
+--debug            Enable debug logs
+--json             Emit machine-readable output where supported
+```
+
+## Local-First Defaults
+
+Athena keeps private documentation local by default.
+
+- The runtime cache lives in `.athena/`.
+- The default embedding provider is local Transformers.js with
+  `mixedbread-ai/mxbai-embed-xsmall-v1`.
+- PDF ingestion uses the published `pdf-2-llm` package.
+- Athena owns its agent loop; no SDK controls tool selection, step limits,
+  memory, or citation validation.
+- Remote embedding or chat providers require explicit configuration before
+  document text can leave the machine.
+
+## Configuration
+
+Athena discovers `athena.config.ts`, `athena.config.mjs`, or
+`athena.config.json` from the project root.
+
+```ts
+import { defineConfig } from "@alextis59/athena";
+
+export default defineConfig({
+  index: {
+    include: ["**/*.md", "**/*.mdx", "**/*.pdf", "**/*.html"],
+    exclude: ["node_modules/**", "dist/**", ".git/**"]
+  },
+  embeddings: {
+    provider: "transformers-js",
+    model: "mixedbread-ai/mxbai-embed-xsmall-v1",
+    dimensions: 384,
+    pooling: "mean",
+    normalize: true,
+    allowRemoteDocumentText: false
+  },
+  chat: {
+    provider: "none",
+    model: null,
+    allowRemoteDocumentText: false
+  }
+});
+```
+
+Optional embedding providers are `ollama`, `openai`, `voyage`, `cohere`, and
+`gemini`. Cloud providers require `allowRemoteDocumentText: true` and their API
+key environment variable:
+
+- `OPENAI_API_KEY`
+- `VOYAGE_API_KEY`
+- `COHERE_API_KEY`
+- `GEMINI_API_KEY`
+
+Ollama uses the local `/api/embed` endpoint and honors `OLLAMA_HOST` when set.
+
+## Citations
+
+Answers are required to cite retrieved source material. Athena validates
+Markdown line ranges, PDF page and region metadata, source visibility during the
+turn, and out-of-range citations before accepting an answer.
+
+PDF citations include page, region, confidence, and warning metadata when
+available. Low-confidence PDF regions are surfaced as uncertain in the UI.
+
+## MCP Integration
+
+`athena mcp` exposes read-only retrieval tools for external coding agents:
+
+- `searchDocs`
+- `readSourceRange`
+- `readPdfSource`
+- `grepDocs`
+- `listDocs`
+- `relatedChunks`
+
+See [docs/mcp-integration.md](docs/mcp-integration.md) for OpenCode and generic
+MCP setup examples.
+
+## Development
+
+```bash
+npm run format:check
+npm run lint
+npm run typecheck
+npm test
+npm run build
+npm run eval
+```
+
+The offline evaluation validates the committed corpus manifest, ground-truth
+questions, supported document types, hybrid retrieval behavior, PDF handling,
+and answer citation policy.

package/dist/agent/ask.d.ts

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+import type { AgentEvent, AgentTurnInput, AgentTurnResult } from "./types.js";
+export interface AskQuestionInput extends AgentTurnInput {
+    onEvent?: (event: AgentEvent) => void | Promise<void>;
+}
+export declare function askQuestion(input: AskQuestionInput): Promise<AgentTurnResult>;
+export declare function renderTerminalCitations(answer: string): string;
+//# sourceMappingURL=ask.d.ts.map

package/dist/agent/ask.d.ts.map

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package/dist/agent/ask.js

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+import { parseAnswerCitations } from "./citations.js";
+import { runAgentTurn } from "./loop.js";
+export async function askQuestion(input) {
+    let result = null;
+    for await (const event of runAgentTurn(input)) {
+        await input.onEvent?.(event);
+        if (event.type === "complete") {
+            result = {
+                answer: event.answer,
+                finishReason: event.finishReason
+            };
+        }
+    }
+    if (result === null) {
+        return {
+            answer: "",
+            finishReason: "stop"
+        };
+    }
+    return result;
+}
+export function renderTerminalCitations(answer) {
+    const citations = parseAnswerCitations(answer);
+    if (citations.length === 0) {
+        return "";
+    }
+    return [
+        "",
+        "",
+        "Citations:",
+        ...citations.map((citation) => `- ${citation.label}`),
+        ""
+    ].join("\n");
+}
+//# sourceMappingURL=ask.js.map

package/dist/agent/ask.js.map

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package/dist/agent/citations.d.ts

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+import type { RetrievalToolRuntime } from "../retrieval/index.js";
+import type { Citation } from "../shared/types.js";
+export interface ParsedTextCitation {
+    label: string;
+    path: string;
+    startLine: number;
+    endLine: number;
+}
+export interface ParsedPdfCitation {
+    label: string;
+    path: string;
+    page: number;
+    regionId?: string;
+}
+export type ParsedCitation = ParsedTextCitation | ParsedPdfCitation;
+export interface ValidateAnswerCitationsInput {
+    root: string;
+    answer: string;
+    runtime: RetrievalToolRuntime;
+}
+export declare function parseTextCitations(answer: string): ParsedTextCitation[];
+export declare function parsePdfCitations(answer: string): ParsedPdfCitation[];
+export declare function parseAnswerCitations(answer: string): ParsedCitation[];
+export declare function serializeTextCitation(citation: ParsedTextCitation): string;
+export declare function serializePdfCitation(citation: ParsedPdfCitation): string;
+export declare function validateAnswerCitations(input: ValidateAnswerCitationsInput): Promise<Citation[]>;
+//# sourceMappingURL=citations.d.ts.map

package/dist/agent/citations.d.ts.map

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package/dist/agent/citations.js

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+import { readFile } from "node:fs/promises";
+import path from "node:path";
+import { UserFacingError } from "../errors.js";
+const textCitationPattern = /\[([^\]\n:]+(?:\/[^\]\n:]+)*):(\d+)-(\d+)\]/gu;
+const pdfCitationPattern = /\[([^\]\n]+?\.pdf)\s+p\.(\d+)(?:#([^\]\n\s]+))?\]/giu;
+export function parseTextCitations(answer) {
+    return parseTextCitationMatches(answer).map((match) => match.citation);
+}
+export function parsePdfCitations(answer) {
+    return parsePdfCitationMatches(answer).map((match) => match.citation);
+}
+export function parseAnswerCitations(answer) {
+    return [
+        ...parseTextCitationMatches(answer),
+        ...parsePdfCitationMatches(answer)
+    ]
+        .sort((left, right) => left.index - right.index)
+        .map((match) => match.citation);
+}
+export function serializeTextCitation(citation) {
+    return `[${citation.path}:${String(citation.startLine)}-${String(citation.endLine)}]`;
+}
+export function serializePdfCitation(citation) {
+    const region = citation.regionId === undefined ? "" : `#${citation.regionId}`;
+    return `[${citation.path} p.${String(citation.page)}${region}]`;
+}
+export async function validateAnswerCitations(input) {
+    const parsed = parseAnswerCitations(input.answer);
+    if (parsed.length === 0) {
+        if (requiresCitation(input.answer)) {
+            throw new UserFacingError("Athena answer requires at least one source citation.");
+        }
+        return [];
+    }
+    const citations = [];
+    for (const parsedCitation of parsed) {
+        validateCitationSourcePath(parsedCitation.label, parsedCitation.path);
+        const indexedSource = input.runtime.getDoc(parsedCitation.path);
+        if (indexedSource === null) {
+            throw new UserFacingError(`Citation path is not indexed: ${parsedCitation.path}`);
+        }
+        if (isParsedPdfCitation(parsedCitation)) {
+            validatePdfCitation(parsedCitation);
+            if (indexedSource.kind !== "pdf") {
+                throw new UserFacingError(`Citation path is not a PDF: ${parsedCitation.path}`);
+            }
+            const locator = findReadPdfLocator(input.runtime.trace.readLocators, parsedCitation);
+            if (locator === null) {
+                throw new UserFacingError(`Citation was not retrieved or read during this turn: ${parsedCitation.label}`);
+            }
+            citations.push({
+                label: parsedCitation.label,
+                locator
+            });
+            continue;
+        }
+        validateTextCitation(parsedCitation);
+        if (indexedSource.kind === "pdf") {
+            throw new UserFacingError(`PDF citations must use page labels: ${parsedCitation.label}`);
+        }
+        const locator = {
+            type: "text",
+            path: parsedCitation.path,
+            startLine: parsedCitation.startLine,
+            endLine: parsedCitation.endLine
+        };
+        await validateLineBounds(input.root, locator);
+        if (!wasTextReadDuringTurn(input.runtime.trace.readLocators, locator)) {
+            throw new UserFacingError(`Citation was not retrieved or read during this turn: ${parsedCitation.label}`);
+        }
+        citations.push({
+            label: parsedCitation.label,
+            locator
+        });
+    }
+    return citations;
+}
+function parseTextCitationMatches(answer) {
+    const citations = [];
+    for (const match of answer.matchAll(textCitationPattern)) {
+        const label = match[0];
+        const sourcePath = match[1];
+        const startLine = Number(match[2]);
+        const endLine = Number(match[3]);
+        if (sourcePath === undefined ||
+            !Number.isInteger(startLine) ||
+            !Number.isInteger(endLine)) {
+            continue;
+        }
+        citations.push({
+            index: match.index ?? 0,
+            citation: {
+                label,
+                path: sourcePath,
+                startLine,
+                endLine
+            }
+        });
+    }
+    return citations;
+}
+function parsePdfCitationMatches(answer) {
+    const citations = [];
+    for (const match of answer.matchAll(pdfCitationPattern)) {
+        const label = match[0];
+        const sourcePath = match[1];
+        const page = Number(match[2]);
+        const regionId = match[3];
+        if (sourcePath === undefined ||
+            !Number.isInteger(page) ||
+            page < 1 ||
+            page > Number.MAX_SAFE_INTEGER) {
+            continue;
+        }
+        const citation = {
+            label,
+            path: sourcePath.trim(),
+            page
+        };
+        if (regionId !== undefined) {
+            citation.regionId = regionId;
+        }
+        citations.push({
+            index: match.index ?? 0,
+            citation
+        });
+    }
+    return citations;
+}
+function isParsedPdfCitation(citation) {
+    return "page" in citation;
+}
+function validateCitationSourcePath(label, sourcePath) {
+    if (sourcePath.trim() === "" ||
+        sourcePath.includes("..") ||
+        path.isAbsolute(sourcePath)) {
+        throw new UserFacingError(`Citation path must be repository-relative: ${label}`);
+    }
+}
+function validateTextCitation(citation) {
+    if (citation.startLine < 1 || citation.endLine < citation.startLine) {
+        throw new UserFacingError(`Citation line range is invalid: ${citation.label}`);
+    }
+}
+function validatePdfCitation(citation) {
+    if (!Number.isInteger(citation.page) || citation.page < 1) {
+        throw new UserFacingError(`PDF citation page is invalid: ${citation.label}`);
+    }
+    if (citation.regionId !== undefined && citation.regionId.trim() === "") {
+        throw new UserFacingError(`PDF citation region is invalid: ${citation.label}`);
+    }
+}
+async function validateLineBounds(root, locator) {
+    const fileText = await readFile(path.join(root, locator.path), "utf8");
+    const lineCount = fileText.replace(/\r\n?/gu, "\n").split("\n").length;
+    if (locator.endLine > lineCount) {
+        throw new UserFacingError(`Citation line range is outside ${locator.path}: ${String(locator.startLine)}-${String(locator.endLine)}`);
+    }
+}
+function wasTextReadDuringTurn(readLocators, locator) {
+    return readLocators.some((readLocator) => readLocator.type === "text" &&
+        readLocator.path === locator.path &&
+        locator.startLine >= readLocator.startLine &&
+        locator.endLine <= readLocator.endLine);
+}
+function findReadPdfLocator(readLocators, citation) {
+    const candidates = readLocators.filter((readLocator) => readLocator.type === "pdf" &&
+        readLocator.path === citation.path &&
+        readLocator.page === citation.page);
+    if (citation.regionId === undefined) {
+        return candidates[0] ?? null;
+    }
+    return (candidates.find((locator) => locator.regionId === citation.regionId) ?? null);
+}
+function requiresCitation(answer) {
+    const normalized = answer.trim().toLowerCase();
+    if (normalized === "") {
+        return false;
+    }
+    return ![
+        "could not",
+        "cannot",
+        "unable",
+        "not enough evidence",
+        "not verified",
+        "no indexed source",
+        "tool budget"
+    ].some((marker) => normalized.includes(marker));
+}
+//# sourceMappingURL=citations.js.map

package/dist/agent/citations.js.map

@@ -0,0 +1 @@
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package/dist/agent/fake-provider.d.ts

@@ -0,0 +1,9 @@
+import type { ModelEvent, ModelProvider, ModelProviderRequest } from "./types.js";
+export declare class FakeModelProvider implements ModelProvider {
+    readonly requests: ModelProviderRequest[];
+    private readonly responses;
+    constructor(responses?: Iterable<readonly ModelEvent[]>);
+    enqueue(response: readonly ModelEvent[]): void;
+    streamResponse(input: ModelProviderRequest): AsyncIterable<ModelEvent>;
+}
+//# sourceMappingURL=fake-provider.d.ts.map

package/dist/agent/fake-provider.d.ts.map

@@ -0,0 +1 @@
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package/dist/agent/fake-provider.js

@@ -0,0 +1,51 @@
+export class FakeModelProvider {
+    requests = [];
+    responses;
+    constructor(responses = []) {
+        this.responses = [...responses].map((response) => [...response]);
+    }
+    enqueue(response) {
+        this.responses.push([...response]);
+    }
+    async *streamResponse(input) {
+        this.requests.push(cloneRequest(input));
+        await Promise.resolve();
+        for (const event of this.responses.shift() ?? [
+            { type: "complete", finishReason: "stop" }
+        ]) {
+            yield event;
+        }
+    }
+}
+function cloneRequest(input) {
+    const request = {
+        model: input.model,
+        messages: input.messages.map(cloneMessage),
+        tools: input.tools.map(cloneTool)
+    };
+    if (input.temperature !== undefined) {
+        request.temperature = input.temperature;
+    }
+    return request;
+}
+function cloneMessage(message) {
+    if (message.role !== "assistant") {
+        return { ...message };
+    }
+    const clone = {
+        role: "assistant",
+        content: message.content
+    };
+    if (message.toolCalls !== undefined) {
+        clone.toolCalls = message.toolCalls.map((toolCall) => ({ ...toolCall }));
+    }
+    return clone;
+}
+function cloneTool(tool) {
+    return {
+        name: tool.name,
+        description: tool.description,
+        inputSchema: { ...tool.inputSchema }
+    };
+}
+//# sourceMappingURL=fake-provider.js.map

package/dist/agent/fake-provider.js.map

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

@@ -0,0 +1,10 @@
+export { FakeModelProvider } from "./fake-provider.js";
+export { askQuestion, renderTerminalCitations } from "./ask.js";
+export type { AskQuestionInput } from "./ask.js";
+export { parseAnswerCitations, parsePdfCitations, parseTextCitations, serializePdfCitation, serializeTextCitation, validateAnswerCitations } from "./citations.js";
+export type { ParsedCitation, ParsedPdfCitation, ParsedTextCitation, ValidateAnswerCitationsInput } from "./citations.js";
+export { DEFAULT_MAX_AGENT_STEPS, buildModelMessages, createModelToolDefinitions, runAgentTurn } from "./loop.js";
+export { OllamaModelProvider, createConfiguredModelProvider, validateModelProviderConfig } from "./providers.js";
+export type { CreateModelProviderOptions, FetchLike } from "./providers.js";
+export type { AssistantModelMessage, AgentEvent, AgentTurnInput, AgentTurnResult, CompactConversationTurn, ModelEvent, ModelFinishReason, ModelMessage, ModelProvider, ModelProviderRequest, ModelRole, ModelToolCall, ModelToolCallEvent, ModelToolDefinition, ModelToolResultMessage, TextModelMessage } from "./types.js";
+//# sourceMappingURL=index.d.ts.map

package/dist/agent/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/agent/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,iBAAiB,EAAE,MAAM,oBAAoB,CAAC;AACvD,OAAO,EAAE,WAAW,EAAE,uBAAuB,EAAE,MAAM,UAAU,CAAC;AAChE,YAAY,EAAE,gBAAgB,EAAE,MAAM,UAAU,CAAC;AACjD,OAAO,EACL,oBAAoB,EACpB,iBAAiB,EACjB,kBAAkB,EAClB,oBAAoB,EACpB,qBAAqB,EACrB,uBAAuB,EACxB,MAAM,gBAAgB,CAAC;AACxB,YAAY,EACV,cAAc,EACd,iBAAiB,EACjB,kBAAkB,EAClB,4BAA4B,EAC7B,MAAM,gBAAgB,CAAC;AACxB,OAAO,EACL,uBAAuB,EACvB,kBAAkB,EAClB,0BAA0B,EAC1B,YAAY,EACb,MAAM,WAAW,CAAC;AACnB,OAAO,EACL,mBAAmB,EACnB,6BAA6B,EAC7B,2BAA2B,EAC5B,MAAM,gBAAgB,CAAC;AACxB,YAAY,EAAE,0BAA0B,EAAE,SAAS,EAAE,MAAM,gBAAgB,CAAC;AAC5E,YAAY,EACV,qBAAqB,EACrB,UAAU,EACV,cAAc,EACd,eAAe,EACf,uBAAuB,EACvB,UAAU,EACV,iBAAiB,EACjB,YAAY,EACZ,aAAa,EACb,oBAAoB,EACpB,SAAS,EACT,aAAa,EACb,kBAAkB,EAClB,mBAAmB,EACnB,sBAAsB,EACtB,gBAAgB,EACjB,MAAM,YAAY,CAAC"}

package/dist/agent/index.js

@@ -0,0 +1,6 @@
+export { FakeModelProvider } from "./fake-provider.js";
+export { askQuestion, renderTerminalCitations } from "./ask.js";
+export { parseAnswerCitations, parsePdfCitations, parseTextCitations, serializePdfCitation, serializeTextCitation, validateAnswerCitations } from "./citations.js";
+export { DEFAULT_MAX_AGENT_STEPS, buildModelMessages, createModelToolDefinitions, runAgentTurn } from "./loop.js";
+export { OllamaModelProvider, createConfiguredModelProvider, validateModelProviderConfig } from "./providers.js";
+//# sourceMappingURL=index.js.map

package/dist/agent/index.js.map

@@ -0,0 +1 @@
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package/dist/agent/loop.d.ts

@@ -0,0 +1,11 @@
+import { createModelToolDefinitions } from "./tools.js";
+import type { AgentEvent, AgentTurnInput, CompactConversationTurn, ModelMessage } from "./types.js";
+export declare const DEFAULT_MAX_AGENT_STEPS = 6;
+export declare function runAgentTurn(input: AgentTurnInput): AsyncIterable<AgentEvent>;
+export declare function buildModelMessages(input: {
+    question: string;
+    previousTurns?: CompactConversationTurn[];
+    pinnedSources?: string[];
+}): ModelMessage[];
+export { createModelToolDefinitions };
+//# sourceMappingURL=loop.d.ts.map

package/dist/agent/loop.d.ts.map

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