@alextis59/athena 1.1.0 → 1.3.0

package/README.md

@@ -53,7 +53,7 @@ Common options:
 --port <port>      Server port
 --agent-provider <opencode|codex>
                    External agent provider for MCP
---debug            Enable debug logs
+--debug            Enable debug logs and write index traces to /tmp/athena-traces
 --json             Emit machine-readable output where supported
 ```
 
@@ -133,10 +133,11 @@ available. Low-confidence PDF regions are surfaced as uncertain in the UI.
 - `listDocs`
 - `relatedChunks`
 
-See [docs/mcp-integration.md](docs/mcp-integration.md) for OpenCode, Codex, and
-generic MCP setup examples. OpenCode is the default external-agent provider;
-pass `athena mcp --agent-provider codex` or set `agent.provider: "codex"` when
-configuring Athena for Codex.
+See the
+[MCP integration guide](https://github.com/alextis59/athena/blob/main/docs/mcp-integration.md)
+for OpenCode, Codex, and generic MCP setup examples. OpenCode is the default
+external-agent provider; pass `athena mcp --agent-provider codex` or set
+`agent.provider: "codex"` when configuring Athena for Codex.
 
 ## Development
 

package/dist/cli/help.js

@@ -21,7 +21,7 @@ Options:
   --port <port>      Server port (default: 4317)
   --agent-provider <opencode|codex>
                      External agent provider for MCP (default: opencode)
-  --debug            Enable debug logs
+  --debug            Enable debug logs and write index traces to /tmp/athena-traces
   --json             Emit machine-readable output where supported
   --build            Build the index before serving
   -h, --help         Show help

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

@@ -1 +1 @@
-{"version":3,"file":"run.d.ts","sourceRoot":"","sources":["../../src/cli/run.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAkC,MAAM,cAAc,CAAC;AAexE,OAAO,KAAK,EAAkB,aAAa,EAAE,MAAM,mBAAmB,CAAC;AAMvE,MAAM,WAAW,UAAU;IACzB,KAAK,CAAC,EAAE,aAAa,CAAC,MAAM,GAAG,UAAU,CAAC,CAAC;IAC3C,MAAM,EAAE,WAAW,CAAC;IACpB,MAAM,EAAE,WAAW,CAAC;CACrB;AAED,MAAM,WAAW,WAAW;IAC1B,KAAK,CAAC,KAAK,EAAE,MAAM,GAAG,UAAU,GAAG,OAAO,CAAC;CAC5C;AAED,MAAM,WAAW,cAAc;IAC7B,GAAG,EAAE,MAAM,CAAC;IACZ,aAAa,CAAC,EAAE,aAAa,CAAC;IAC9B,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,qBAAqB,CAAC,EAAE,OAAO,CAAC;CACjC;AAED,MAAM,WAAW,SAAS;IACxB,QAAQ,EAAE,QAAQ,CAAC;CACpB;AAED,wBAAsB,MAAM,CAC1B,IAAI,EAAE,MAAM,EAAE,EACd,OAAO,EAAE,UAAU,EACnB,WAAW,EAAE,cAAc,GAC1B,OAAO,CAAC,SAAS,CAAC,CAqBpB"}
+{"version":3,"file":"run.d.ts","sourceRoot":"","sources":["../../src/cli/run.ts"],"names":[],"mappings":"AAKA,OAAO,EAAE,QAAQ,EAAkC,MAAM,cAAc,CAAC;AAexE,OAAO,KAAK,EAAkB,aAAa,EAAE,MAAM,mBAAmB,CAAC;AAOvE,MAAM,WAAW,UAAU;IACzB,KAAK,CAAC,EAAE,aAAa,CAAC,MAAM,GAAG,UAAU,CAAC,CAAC;IAC3C,MAAM,EAAE,WAAW,CAAC;IACpB,MAAM,EAAE,WAAW,CAAC;CACrB;AAED,MAAM,WAAW,WAAW;IAC1B,KAAK,CAAC,KAAK,EAAE,MAAM,GAAG,UAAU,GAAG,OAAO,CAAC;CAC5C;AAED,MAAM,WAAW,cAAc;IAC7B,GAAG,EAAE,MAAM,CAAC;IACZ,aAAa,CAAC,EAAE,aAAa,CAAC;IAC9B,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,qBAAqB,CAAC,EAAE,OAAO,CAAC;CACjC;AAED,MAAM,WAAW,SAAS;IACxB,QAAQ,EAAE,QAAQ,CAAC;CACpB;AAED,wBAAsB,MAAM,CAC1B,IAAI,EAAE,MAAM,EAAE,EACd,OAAO,EAAE,UAAU,EACnB,WAAW,EAAE,cAAc,GAC1B,OAAO,CAAC,SAAS,CAAC,CAqBpB"}

package/dist/cli/run.js

@@ -1,3 +1,7 @@
+import { randomUUID } from "node:crypto";
+import { appendFile, mkdir, writeFile } from "node:fs/promises";
+import { tmpdir } from "node:os";
+import path from "node:path";
 import { ExitCode, toAthenaError, UserFacingError } from "../errors.js";
 import { askQuestion, renderTerminalCitations } from "../agent/index.js";
 import { loadConfig } from "../config/index.js";
@@ -73,12 +77,121 @@ async function runServeCommand(parsed, streams, environment, logger) {
     });
 }
 async function runIndexCommand(parsed, streams, logger) {
-    const result = await indexFromCliOptions(parsed.options, parsed.options.json
-        ? undefined
-        : (event) => {
-            logger.info(renderIndexProgress(event));
-        });
-    streams.stdout.write(renderIndexResult(result, parsed.options.json));
+    const trace = parsed.options.debug
+        ? await createIndexDebugTrace(logger)
+        : undefined;
+    if (trace !== undefined) {
+        logger.debug(`Index debug trace: ${trace.path}`);
+    }
+    try {
+        const result = await indexFromCliOptions(parsed.options, parsed.options.json
+            ? undefined
+            : (event) => {
+                logger.info(renderIndexProgress(event));
+            }, trace === undefined ? undefined : (event) => trace.record(event));
+        const outputResult = trace === undefined ? result : { ...result, debugTracePath: trace.path };
+        if (trace !== undefined) {
+            logger.debug(`Index debug trace written: ${trace.path}`);
+        }
+        streams.stdout.write(renderIndexResult(outputResult, parsed.options.json));
+    }
+    catch (error) {
+        if (trace !== undefined) {
+            logger.debug(`Index debug trace written: ${trace.path}`);
+        }
+        throw error;
+    }
+}
+async function createIndexDebugTrace(logger) {
+    const directory = path.join(tmpdir(), "athena-traces");
+    const tracePath = path.join(directory, `index-${new Date().toISOString().replace(/[:.]/gu, "-")}-${randomUUID()}.ndjson`);
+    await mkdir(directory, { recursive: true });
+    await writeFile(tracePath, "", "utf8");
+    return {
+        path: tracePath,
+        async record(event) {
+            logger.debug(renderIndexTraceEvent(event));
+            try {
+                await appendFile(tracePath, `${JSON.stringify(event)}\n`, "utf8");
+            }
+            catch (error) {
+                logger.error(`Could not write index debug trace: ${String(error)}`);
+            }
+        }
+    };
+}
+function renderIndexTraceEvent(event) {
+    switch (event.type) {
+        case "index_start":
+            return `Indexing ${readTraceString(event, "root") ?? "root"} into ${readTraceString(event, "databasePath") ?? "database"}`;
+        case "discovery_complete":
+            return `Discovered ${String(readTraceNumber(event, "discovered") ?? 0)} source(s)`;
+        case "source_state":
+            return [
+                `Source ${readTracePath(event)}:`,
+                `kind=${readTraceString(event, "kind") ?? "unknown"}`,
+                `size=${String(readTraceNumber(event, "sizeBytes") ?? 0)} bytes`,
+                `hash=${readTraceString(event, "contentHash") ?? "unknown"}`,
+                `parser=${readTraceString(event, "parserName") ?? "unknown"}@${readTraceString(event, "parserVersion") ?? "unknown"}`,
+                `options=${readTraceString(event, "parserOptionsHash") ?? "unknown"}`
+            ].join(" ");
+        case "source_skipped":
+            return `Skipped ${readTracePath(event)} (unchanged: content hash, parser, version, and parser options match the existing index)`;
+        case "source_parse_start":
+            return `Parsing ${readTracePath(event)} with ${readTraceString(event, "parserName") ?? "parser"}`;
+        case "source_parse_success":
+            return [
+                `Parsed ${readTracePath(event)}`,
+                `(${String(readTraceNumber(event, "blocks") ?? 0)} blocks,`,
+                `${String(readTraceArrayLength(event, "warnings"))} warnings,`,
+                `${String(readTraceArrayLength(event, "artifacts"))} artifacts)`
+            ].join(" ");
+        case "source_parse_skipped":
+            return `Skipped parsing ${readTracePath(event)} (${readTraceString(event, "reason") ?? "no parser result"})`;
+        case "source_parse_failed":
+            return `Failed parsing ${readTracePath(event)}: ${renderTraceError(event.error)}`;
+        case "source_deleted":
+            return `Deleted ${readTracePath(event)} from the index (${readTraceString(event, "reason") ?? "not discovered"})`;
+        case "embedding_sync_start":
+            return "Synchronizing embeddings";
+        case "embedding_sync_complete":
+            return `Synchronized embeddings: ${String(readTraceNumber(event, "embedded") ?? 0)} new vector(s)`;
+        case "index_success":
+            return `Index run ${readTraceString(event, "runId") ?? "completed"} succeeded`;
+        case "index_failed":
+            return `Index run ${readTraceString(event, "runId") ?? "failed"} failed: ${renderTraceError(event.error)}`;
+        default:
+            return `Index trace event: ${event.type}`;
+    }
+}
+function readTracePath(event) {
+    return readTraceString(event, "path") ?? "<unknown>";
+}
+function readTraceString(event, key) {
+    const value = event[key];
+    return typeof value === "string" ? value : undefined;
+}
+function readTraceNumber(event, key) {
+    const value = event[key];
+    return typeof value === "number" && Number.isFinite(value)
+        ? value
+        : undefined;
+}
+function readTraceArrayLength(event, key) {
+    const value = event[key];
+    return Array.isArray(value) ? value.length : 0;
+}
+function renderTraceError(error) {
+    if (typeof error !== "object" || error === null) {
+        return String(error);
+    }
+    const record = error;
+    const message = typeof record.message === "string" ? record.message : "Unknown trace error";
+    const cause = record.cause;
+    if (cause === undefined) {
+        return message;
+    }
+    return `${message}; caused by ${renderTraceError(cause)}`;
 }
 function assertIndexReady(parsed) {
     const database = inspectDatabase(parsed.options.root, parsed.options.db);

package/dist/cli/run.js.map

@@ -1 +1 @@
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package/dist/indexer/index.d.ts

@@ -3,5 +3,5 @@ export { hashFile, hashString } from "./hash.js";
 export { classifySourceKind, isSupportedSourceKind } from "./kinds.js";
 export { indexFromCliOptions, indexRoot, renderIndexProgress, renderIndexResult } from "./run.js";
 export type { DiscoveredSource } from "./discovery.js";
-export type { IndexCounts, IndexProgressEvent, IndexProgressReporter, IndexResult, IndexRootOptions } from "./run.js";
+export type { IndexCounts, IndexProgressEvent, IndexProgressReporter, IndexResult, IndexRootOptions, IndexTraceEvent, IndexTraceReporter, SerializedTraceError } from "./run.js";
 //# sourceMappingURL=index.d.ts.map

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

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/indexer/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,eAAe,EAAE,qBAAqB,EAAE,MAAM,gBAAgB,CAAC;AACxE,OAAO,EAAE,QAAQ,EAAE,UAAU,EAAE,MAAM,WAAW,CAAC;AACjD,OAAO,EAAE,kBAAkB,EAAE,qBAAqB,EAAE,MAAM,YAAY,CAAC;AACvE,OAAO,EACL,mBAAmB,EACnB,SAAS,EACT,mBAAmB,EACnB,iBAAiB,EAClB,MAAM,UAAU,CAAC;AAClB,YAAY,EAAE,gBAAgB,EAAE,MAAM,gBAAgB,CAAC;AACvD,YAAY,EACV,WAAW,EACX,kBAAkB,EAClB,qBAAqB,EACrB,WAAW,EACX,gBAAgB,EACjB,MAAM,UAAU,CAAC"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/indexer/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,eAAe,EAAE,qBAAqB,EAAE,MAAM,gBAAgB,CAAC;AACxE,OAAO,EAAE,QAAQ,EAAE,UAAU,EAAE,MAAM,WAAW,CAAC;AACjD,OAAO,EAAE,kBAAkB,EAAE,qBAAqB,EAAE,MAAM,YAAY,CAAC;AACvE,OAAO,EACL,mBAAmB,EACnB,SAAS,EACT,mBAAmB,EACnB,iBAAiB,EAClB,MAAM,UAAU,CAAC;AAClB,YAAY,EAAE,gBAAgB,EAAE,MAAM,gBAAgB,CAAC;AACvD,YAAY,EACV,WAAW,EACX,kBAAkB,EAClB,qBAAqB,EACrB,WAAW,EACX,gBAAgB,EAChB,eAAe,EACf,kBAAkB,EAClB,oBAAoB,EACrB,MAAM,UAAU,CAAC"}

package/dist/indexer/run.d.ts

@@ -15,6 +15,7 @@ export interface IndexResult {
     databasePath: string;
     runId: string;
     counts: IndexCounts;
+    debugTracePath?: string;
 }
 export interface IndexProgressEvent {
     type: "embedding_batch";
@@ -28,15 +29,29 @@ export interface IndexProgressEvent {
     model: string;
 }
 export type IndexProgressReporter = (event: IndexProgressEvent) => void;
-export declare function indexFromCliOptions(options: CliOptions, onProgress?: IndexProgressReporter): Promise<IndexResult>;
+export interface SerializedTraceError {
+    name: string;
+    message: string;
+    stack?: string;
+    cause?: SerializedTraceError;
+}
+export interface IndexTraceEvent {
+    type: string;
+    timestamp: string;
+    [key: string]: unknown;
+}
+export type IndexTraceReporter = (event: IndexTraceEvent) => void | Promise<void>;
+export declare function indexFromCliOptions(options: CliOptions, onProgress?: IndexProgressReporter, onTrace?: IndexTraceReporter): Promise<IndexResult>;
 export interface IndexRootOptions {
     root: string;
     dbPath?: string;
     loadedConfig?: LoadedConfig;
     onProgress?: IndexProgressReporter;
+    onTrace?: IndexTraceReporter;
     pdfConverter?: Pdf2LlmConverter;
 }
 export declare function indexRoot(options: IndexRootOptions): Promise<IndexResult>;
 export declare function renderIndexResult(result: IndexResult, json: boolean): string;
 export declare function renderIndexProgress(event: IndexProgressEvent): string;
+export declare function serializeTraceError(error: unknown): SerializedTraceError;
 //# sourceMappingURL=run.d.ts.map

package/dist/indexer/run.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"run.d.ts","sourceRoot":"","sources":["../../src/indexer/run.ts"],"names":[],"mappings":"AA2BA,OAAO,KAAK,EAAE,UAAU,EAAE,MAAM,mBAAmB,CAAC;AACpD,OAAO,KAAK,EAAE,YAAY,EAAa,MAAM,oBAAoB,CAAC;AAWlE,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,qBAAqB,CAAC;AAK5D,MAAM,WAAW,WAAW;IAC1B,UAAU,EAAE,MAAM,CAAC;IACnB,OAAO,EAAE,MAAM,CAAC;IAChB,MAAM,EAAE,MAAM,CAAC;IACf,QAAQ,EAAE,MAAM,CAAC;IACjB,MAAM,EAAE,MAAM,CAAC;IACf,SAAS,EAAE,MAAM,CAAC;IAClB,OAAO,EAAE,MAAM,CAAC;CACjB;AAED,MAAM,WAAW,WAAW;IAC1B,IAAI,EAAE,MAAM,CAAC;IACb,YAAY,EAAE,MAAM,CAAC;IACrB,KAAK,EAAE,MAAM,CAAC;IACd,MAAM,EAAE,WAAW,CAAC;CACrB;AAED,MAAM,WAAW,kBAAkB;IACjC,IAAI,EAAE,iBAAiB,CAAC;IACxB,WAAW,EAAE,MAAM,CAAC;IACpB,UAAU,EAAE,MAAM,CAAC;IACnB,SAAS,EAAE,MAAM,CAAC;IAClB,SAAS,EAAE,MAAM,CAAC;IAClB,KAAK,EAAE,MAAM,CAAC;IACd,QAAQ,EAAE,MAAM,CAAC;IACjB,QAAQ,EAAE,MAAM,CAAC;IACjB,KAAK,EAAE,MAAM,CAAC;CACf;AAED,MAAM,MAAM,qBAAqB,GAAG,CAAC,KAAK,EAAE,kBAAkB,KAAK,IAAI,CAAC;AA+DxE,wBAAsB,mBAAmB,CACvC,OAAO,EAAE,UAAU,EACnB,UAAU,CAAC,EAAE,qBAAqB,GACjC,OAAO,CAAC,WAAW,CAAC,CAuBtB;AAED,MAAM,WAAW,gBAAgB;IAC/B,IAAI,EAAE,MAAM,CAAC;IACb,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,YAAY,CAAC,EAAE,YAAY,CAAC;IAC5B,UAAU,CAAC,EAAE,qBAAqB,CAAC;IACnC,YAAY,CAAC,EAAE,gBAAgB,CAAC;CACjC;AAED,wBAAsB,SAAS,CAC7B,OAAO,EAAE,gBAAgB,GACxB,OAAO,CAAC,WAAW,CAAC,CA+JtB;AAED,wBAAgB,iBAAiB,CAAC,MAAM,EAAE,WAAW,EAAE,IAAI,EAAE,OAAO,GAAG,MAAM,CAkB5E;AAED,wBAAgB,mBAAmB,CAAC,KAAK,EAAE,kBAAkB,GAAG,MAAM,CAUrE"}
+{"version":3,"file":"run.d.ts","sourceRoot":"","sources":["../../src/indexer/run.ts"],"names":[],"mappings":"AA2BA,OAAO,KAAK,EAAE,UAAU,EAAE,MAAM,mBAAmB,CAAC;AACpD,OAAO,KAAK,EAAE,YAAY,EAAa,MAAM,oBAAoB,CAAC;AAWlE,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,qBAAqB,CAAC;AAK5D,MAAM,WAAW,WAAW;IAC1B,UAAU,EAAE,MAAM,CAAC;IACnB,OAAO,EAAE,MAAM,CAAC;IAChB,MAAM,EAAE,MAAM,CAAC;IACf,QAAQ,EAAE,MAAM,CAAC;IACjB,MAAM,EAAE,MAAM,CAAC;IACf,SAAS,EAAE,MAAM,CAAC;IAClB,OAAO,EAAE,MAAM,CAAC;CACjB;AAED,MAAM,WAAW,WAAW;IAC1B,IAAI,EAAE,MAAM,CAAC;IACb,YAAY,EAAE,MAAM,CAAC;IACrB,KAAK,EAAE,MAAM,CAAC;IACd,MAAM,EAAE,WAAW,CAAC;IACpB,cAAc,CAAC,EAAE,MAAM,CAAC;CACzB;AAED,MAAM,WAAW,kBAAkB;IACjC,IAAI,EAAE,iBAAiB,CAAC;IACxB,WAAW,EAAE,MAAM,CAAC;IACpB,UAAU,EAAE,MAAM,CAAC;IACnB,SAAS,EAAE,MAAM,CAAC;IAClB,SAAS,EAAE,MAAM,CAAC;IAClB,KAAK,EAAE,MAAM,CAAC;IACd,QAAQ,EAAE,MAAM,CAAC;IACjB,QAAQ,EAAE,MAAM,CAAC;IACjB,KAAK,EAAE,MAAM,CAAC;CACf;AAED,MAAM,MAAM,qBAAqB,GAAG,CAAC,KAAK,EAAE,kBAAkB,KAAK,IAAI,CAAC;AAExE,MAAM,WAAW,oBAAoB;IACnC,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE,MAAM,CAAC;IAChB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,KAAK,CAAC,EAAE,oBAAoB,CAAC;CAC9B;AAED,MAAM,WAAW,eAAe;IAC9B,IAAI,EAAE,MAAM,CAAC;IACb,SAAS,EAAE,MAAM,CAAC;IAClB,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC;CACxB;AAED,MAAM,MAAM,kBAAkB,GAAG,CAC/B,KAAK,EAAE,eAAe,KACnB,IAAI,GAAG,OAAO,CAAC,IAAI,CAAC,CAAC;AA+D1B,wBAAsB,mBAAmB,CACvC,OAAO,EAAE,UAAU,EACnB,UAAU,CAAC,EAAE,qBAAqB,EAClC,OAAO,CAAC,EAAE,kBAAkB,GAC3B,OAAO,CAAC,WAAW,CAAC,CA2BtB;AAED,MAAM,WAAW,gBAAgB;IAC/B,IAAI,EAAE,MAAM,CAAC;IACb,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,YAAY,CAAC,EAAE,YAAY,CAAC;IAC5B,UAAU,CAAC,EAAE,qBAAqB,CAAC;IACnC,OAAO,CAAC,EAAE,kBAAkB,CAAC;IAC7B,YAAY,CAAC,EAAE,gBAAgB,CAAC;CACjC;AAED,wBAAsB,SAAS,CAC7B,OAAO,EAAE,gBAAgB,GACxB,OAAO,CAAC,WAAW,CAAC,CAuQtB;AAED,wBAAgB,iBAAiB,CAAC,MAAM,EAAE,WAAW,EAAE,IAAI,EAAE,OAAO,GAAG,MAAM,CAkB5E;AAED,wBAAgB,mBAAmB,CAAC,KAAK,EAAE,kBAAkB,GAAG,MAAM,CAUrE;AA2DD,wBAAgB,mBAAmB,CAAC,KAAK,EAAE,OAAO,GAAG,oBAAoB,CAsBxE"}

package/dist/indexer/run.js

@@ -12,7 +12,7 @@ const parserOptionsHash = hashString(JSON.stringify({
     parser: "text-line-parser-v1",
     chunking: defaultChunkingOptions
 }));
-export async function indexFromCliOptions(options, onProgress) {
+export async function indexFromCliOptions(options, onProgress, onTrace) {
     const loadedConfig = await loadConfig(options.config === undefined
         ? { root: options.root }
         : { root: options.root, configPath: options.config });
@@ -29,6 +29,9 @@ export async function indexFromCliOptions(options, onProgress) {
     if (onProgress !== undefined) {
         indexOptions.onProgress = onProgress;
     }
+    if (onTrace !== undefined) {
+        indexOptions.onTrace = onTrace;
+    }
     return await indexRoot(indexOptions);
 }
 export async function indexRoot(options) {
@@ -39,8 +42,30 @@ export async function indexRoot(options) {
     const startedAt = new Date().toISOString();
     const counts = createEmptyCounts();
     try {
+        await emitTrace(options.onTrace, {
+            type: "index_start",
+            root: initialized.paths.root,
+            databasePath: initialized.paths.databasePath,
+            runId,
+            configPath: loadedConfig.configPath,
+            index: {
+                include: loadedConfig.config.index.include,
+                exclude: loadedConfig.config.index.exclude
+            },
+            pdf: loadedConfig.config.pdf,
+            embeddings: loadedConfig.config.embeddings
+        });
         const embeddingProvider = createEmbeddingProvider(loadedConfig.config.embeddings);
         const discovered = await discoverSources(initialized.paths.root, loadedConfig.config);
+        await emitTrace(options.onTrace, {
+            type: "discovery_complete",
+            root: initialized.paths.root,
+            discovered: discovered.length,
+            sources: discovered.map((source) => ({
+                path: source.relativePath,
+                kind: source.kind
+            }))
+        });
         const sourceStates = await Promise.all(discovered.map((source) => collectSourceState(initialized.paths.root, source, loadedConfig.config.pdf)));
         const existingSources = listExistingSources(database, initialized.paths.root);
         const discoveredPaths = new Set(sourceStates.map((source) => source.relative_path));
@@ -48,11 +73,28 @@ export async function indexRoot(options) {
         counts.discovered = discovered.length;
         for (const sourceState of sourceStates) {
             const existing = existingSources.get(sourceState.relative_path);
-            if (isUnchanged(existing, sourceState)) {
+            await emitTrace(options.onTrace, {
+                type: "source_state",
+                ...sourceTraceDetails(sourceState),
+                existing: existing === undefined ? null : sourceRowTraceDetails(existing)
+            });
+            if (existing !== undefined && isUnchanged(existing, sourceState)) {
                 counts.skipped += 1;
+                await emitTrace(options.onTrace, {
+                    type: "source_skipped",
+                    reason: "unchanged",
+                    explanation: "content hash, parser, parser version, and parser options match the existing index row",
+                    ...sourceTraceDetails(sourceState),
+                    existingSourceId: existing.id
+                });
                 continue;
             }
             try {
+                await emitTrace(options.onTrace, {
+                    type: "source_parse_start",
+                    ...sourceTraceDetails(sourceState),
+                    existingSourceId: existing?.id ?? null
+                });
                 const parsedDocument = await parseSourceFile(sourceState.absolute_path, sourceState.kind, {
                     pdf: loadedConfig.config.pdf,
                     ...(options.pdfConverter === undefined
@@ -64,6 +106,27 @@ export async function indexRoot(options) {
                     : await materializeParserArtifacts(initialized.paths, sourceState, parsedDocument);
                 if (materializedDocument !== null) {
                     counts.parsed += 1;
+                    await emitTrace(options.onTrace, {
+                        type: "source_parse_success",
+                        ...sourceTraceDetails(sourceState),
+                        blocks: materializedDocument.document.blocks.length,
+                        warnings: materializedDocument.document.warnings.map((warning) => ({
+                            code: warning.code,
+                            message: warning.message
+                        })),
+                        artifacts: materializedDocument.document.artifacts?.map((artifact) => ({
+                            kind: artifact.kind
+                        })) ?? [],
+                        textLength: materializedDocument.document.text.length,
+                        normalizedTextLength: materializedDocument.document.normalizedText.length
+                    });
+                }
+                else {
+                    await emitTrace(options.onTrace, {
+                        type: "source_parse_skipped",
+                        reason: "unsupported_source_kind",
+                        ...sourceTraceDetails(sourceState)
+                    });
                 }
                 updates.push({
                     source: sourceState,
@@ -77,10 +140,16 @@ export async function indexRoot(options) {
             }
             catch (error) {
                 counts.failed += 1;
+                await emitTrace(options.onTrace, {
+                    type: "source_parse_failed",
+                    ...sourceTraceDetails(sourceState),
+                    error: serializeTraceError(error)
+                });
                 throw error;
             }
         }
         const deletedSourceIds = [];
+        const deletedSources = [];
         withTransaction(database, () => {
             for (const update of updates) {
                 upsertSource(database, initialized.paths.root, update.source, update.parsedDocument, update.existingSourceId);
@@ -90,9 +159,17 @@ export async function indexRoot(options) {
                     deleteSource(database, existing.id);
                     counts.deleted += 1;
                     deletedSourceIds.push(existing.id);
+                    deletedSources.push(existing);
                 }
             }
         });
+        for (const deletedSource of deletedSources) {
+            await emitTrace(options.onTrace, {
+                type: "source_deleted",
+                reason: "not_discovered",
+                ...sourceRowTraceDetails(deletedSource)
+            });
+        }
         await Promise.all([
             ...deletedSourceIds.map((sourceId) => removeSourceBlobs(initialized.paths, sourceId)),
             ...updates
@@ -100,7 +177,15 @@ export async function indexRoot(options) {
                 .filter((stagedBlobs) => stagedBlobs !== undefined)
                 .map((stagedBlobs) => commitSourceBlobs(stagedBlobs))
         ]);
+        await emitTrace(options.onTrace, {
+            type: "embedding_sync_start",
+            provider: embeddingProvider?.metadata ?? null
+        });
         counts.embedded = await syncEmbeddings(database, initialized.paths.root, embeddingProvider, options.onProgress);
+        await emitTrace(options.onTrace, {
+            type: "embedding_sync_complete",
+            embedded: counts.embedded
+        });
         withTransaction(database, () => {
             insertRun(database, {
                 id: runId,
@@ -112,6 +197,13 @@ export async function indexRoot(options) {
                 errorMessage: null
             });
         });
+        await emitTrace(options.onTrace, {
+            type: "index_success",
+            root: initialized.paths.root,
+            databasePath: initialized.paths.databasePath,
+            runId,
+            counts
+        });
         return {
             root: initialized.paths.root,
             databasePath: initialized.paths.databasePath,
@@ -120,6 +212,14 @@ export async function indexRoot(options) {
         };
     }
     catch (error) {
+        await emitTrace(options.onTrace, {
+            type: "index_failed",
+            root: initialized.paths.root,
+            databasePath: initialized.paths.databasePath,
+            runId,
+            counts,
+            error: serializeTraceError(error)
+        });
         withTransaction(database, () => {
             insertRun(database, {
                 id: runId,
@@ -177,6 +277,64 @@ function createEmptyCounts() {
         deleted: 0
     };
 }
+async function emitTrace(reporter, event) {
+    if (reporter === undefined) {
+        return;
+    }
+    try {
+        await reporter({
+            timestamp: new Date().toISOString(),
+            ...event
+        });
+    }
+    catch {
+        // Debug tracing must not change indexing behavior.
+    }
+}
+function sourceTraceDetails(source) {
+    return {
+        path: source.relative_path,
+        absolutePath: source.absolute_path,
+        sourceId: source.id,
+        kind: source.kind,
+        sizeBytes: source.size_bytes,
+        modifiedTimeMs: source.modified_time_ms,
+        contentHash: source.content_hash,
+        parserName: source.parser_name,
+        parserVersion: source.parser_version,
+        parserOptionsHash: source.parser_options_hash
+    };
+}
+function sourceRowTraceDetails(source) {
+    return {
+        path: source.relative_path,
+        sourceId: source.id,
+        kind: source.kind,
+        contentHash: source.content_hash,
+        parserName: source.parser_name,
+        parserVersion: source.parser_version,
+        parserOptionsHash: source.parser_options_hash
+    };
+}
+export function serializeTraceError(error) {
+    if (error instanceof Error) {
+        const serialized = {
+            name: error.name,
+            message: error.message
+        };
+        if (error.stack !== undefined) {
+            serialized.stack = error.stack;
+        }
+        if (error.cause !== undefined) {
+            serialized.cause = serializeTraceError(error.cause);
+        }
+        return serialized;
+    }
+    return {
+        name: typeof error,
+        message: String(error)
+    };
+}
 function isUnchanged(existing, next) {
     return (existing !== undefined &&
         existing.id === next.id &&