ralph-hero-knowledge-index 0.1.21 → 0.1.23

package/dist/index.d.ts

@@ -5,7 +5,15 @@ import { FtsSearch } from "./search.js";
 import { VectorSearch } from "./vector-search.js";
 import { HybridSearch } from "./hybrid-search.js";
 import { Traverser } from "./traverse.js";
-export declare function createServer(dbPath: string): {
+/**
+ * Options for `createServer`. When `embedFn` is provided it replaces the
+ * production `embed` import, allowing tests to bypass the HuggingFace model
+ * download.
+ */
+export interface CreateServerOptions {
+    embedFn?: (text: string) => Promise<Float32Array>;
+}
+export declare function createServer(dbPath: string, opts?: CreateServerOptions): {
     server: McpServer;
     db: KnowledgeDB;
     fts: FtsSearch;

package/dist/index.js

@@ -20,12 +20,44 @@ function resolveEnv(name) {
         return undefined;
     return val;
 }
-export function createServer(dbPath) {
+/**
+ * True when the `chunks` table exists in the schema (v3+). When absent,
+ * `knowledge_memory_stats` reports 0 chunks-per-doc percentiles.
+ */
+function chunksTableExists(db) {
+    const row = db.db
+        .prepare("SELECT name FROM sqlite_master WHERE type='table' AND name='chunks'")
+        .get();
+    return row !== undefined;
+}
+/**
+ * True when the `documents.memory_tier` column exists (v3+). Used to decide
+ * whether tier-level stats can be produced from the schema at all.
+ */
+function memoryTierColumnExists(db) {
+    const rows = db.db
+        .prepare("PRAGMA table_info(documents)")
+        .all();
+    return rows.some((r) => r.name === "memory_tier");
+}
+/**
+ * Percentile helper using nearest-rank. For n sorted values returns the value
+ * at index `floor(n * p)` clamped to [0, n-1]. Returns 0 on empty input.
+ * Matches the spec in Phase 8 Task 8.4: "pick index at floor(n*0.5)".
+ */
+function percentile(sortedValues, p) {
+    if (sortedValues.length === 0)
+        return 0;
+    const idx = Math.min(sortedValues.length - 1, Math.max(0, Math.floor(sortedValues.length * p)));
+    return sortedValues[idx];
+}
+export function createServer(dbPath, opts = {}) {
     const server = new McpServer({ name: "ralph-hero-knowledge", version: "0.1.0" });
     const db = new KnowledgeDB(dbPath);
     const fts = new FtsSearch(db);
     const vec = new VectorSearch(db);
-    const hybrid = new HybridSearch(db, fts, vec, embed);
+    const embedImpl = opts.embedFn ?? embed;
+    const hybrid = new HybridSearch(db, fts, vec, embedImpl);
     const traverser = new Traverser(db);
     server.tool("knowledge_search", "Search the knowledge base by keyword, semantic similarity, and tags. Returns ranked documents.", {
         query: z.string().describe("Search query (keywords or natural language)"),
@@ -34,6 +66,16 @@ export function createServer(dbPath) {
         limit: z.number().optional().describe("Max results (default: 10)"),
         includeSuperseded: z.boolean().optional().describe("Include superseded documents (default: false)"),
         brief: z.boolean().optional().describe("Return minimal metadata only (default: false)"),
+        memory_tier: z
+            .enum(["doc", "raw", "reflection", "any"])
+            .optional()
+            .default("any")
+            .describe("Filter by memory tier: 'doc' (curated), 'raw' (dream-loop ingest), 'reflection' (synthesized), 'any' (default)"),
+        return_chunk_meta: z
+            .boolean()
+            .optional()
+            .default(false)
+            .describe("Include chunk_index/char_start/char_end/context_prefix in each hit when chunk data is available"),
     }, async (args) => {
         try {
             const results = await hybrid.search(args.query, {
@@ -41,15 +83,32 @@ export function createServer(dbPath) {
                 type: args.type,
                 limit: args.limit ?? 10,
                 includeSuperseded: args.includeSuperseded,
+                memoryTier: args.memory_tier,
             });
-            const enriched = results.map(r => {
-                const base = { ...r, tags: db.getTags(r.id) };
+            const enriched = results.map((r) => {
+                // Start with the camelCase SearchResult shape so existing callers
+                // keep working, then optionally add snake_case aliases for new
+                // chunk fields and strip them when callers didn't opt in.
+                const { chunkIndex, charStart, charEnd, contextPrefix, bestChunkId, ...rest } = r;
+                const base = { ...rest, tags: db.getTags(r.id) };
+                if (args.return_chunk_meta) {
+                    if (chunkIndex !== undefined)
+                        base.chunk_index = chunkIndex;
+                    if (charStart !== undefined)
+                        base.char_start = charStart;
+                    if (charEnd !== undefined)
+                        base.char_end = charEnd;
+                    if (contextPrefix !== undefined)
+                        base.context_prefix = contextPrefix;
+                    if (bestChunkId !== undefined)
+                        base.best_chunk_id = bestChunkId;
+                }
                 // SearchResult does not carry githubIssue — fetch from documents table
                 const doc = db.getDocument(r.id);
                 if (doc?.githubIssue) {
                     const outcomes = db.getOutcomeSummary(doc.githubIssue);
                     if (outcomes)
-                        return { ...base, outcomes_summary: outcomes };
+                        base.outcomes_summary = outcomes;
                 }
                 return base;
             });
@@ -66,12 +125,25 @@ export function createServer(dbPath) {
         depth: z.number().optional().describe("Max traversal depth (default: 3)"),
         direction: z.enum(["outgoing", "incoming"]).optional().describe("Edge direction (default: outgoing)"),
         brief: z.boolean().optional().describe("Return minimal metadata only (default: false)"),
+        memory_tier: z
+            .enum(["doc", "raw", "reflection", "any"])
+            .optional()
+            .default("any")
+            .describe("Filter traversed nodes by memory tier (default: 'any')"),
     }, async (args) => {
         try {
             const opts = { type: args.type, depth: args.depth ?? 3 };
-            const results = args.direction === "incoming"
+            let results = args.direction === "incoming"
                 ? traverser.traverseIncoming(args.from, opts)
                 : traverser.traverse(args.from, opts);
+            if (args.memory_tier && args.memory_tier !== "any") {
+                const wantedTier = args.memory_tier;
+                results = results.filter((r) => {
+                    const tier = db.getMemoryTier(r.targetId);
+                    // When memory_tier column is absent (pre-v3 DB) treat as "doc"
+                    return (tier ?? "doc") === wantedTier;
+                });
+            }
             const formatted = formatTraverseResults(results, (id) => db.getTags(id), args.brief ?? false);
             return { content: [{ type: "text", text: JSON.stringify(formatted, null, 2) }] };
         }
@@ -79,6 +151,94 @@ export function createServer(dbPath) {
             return { content: [{ type: "text", text: `Error: ${e.message}` }], isError: true };
         }
     });
+    server.tool("knowledge_memory_stats", "Return counts of documents by memory_tier plus chunk percentiles and last-reflection timestamp. Used by the dream-loop to confirm ingest/reflection completion.", {
+        since: z
+            .string()
+            .optional()
+            .describe("ISO timestamp — counts for 'new_since' are computed against this. Defaults to 24 hours ago."),
+    }, async (args) => {
+        try {
+            const since = args.since ?? new Date(Date.now() - 24 * 3600 * 1000).toISOString();
+            const hasTier = memoryTierColumnExists(db);
+            const hasChunks = chunksTableExists(db);
+            const totalRow = db.db
+                .prepare("SELECT COUNT(*) AS c FROM documents")
+                .get();
+            const totalDocuments = totalRow.c;
+            const byTier = {
+                doc: 0,
+                raw: 0,
+                reflection: 0,
+            };
+            const newSince = {
+                doc: 0,
+                raw: 0,
+                reflection: 0,
+            };
+            if (hasTier) {
+                const rows = db.db
+                    .prepare(`SELECT memory_tier AS tier, COUNT(*) AS c
+               FROM documents GROUP BY memory_tier`)
+                    .all();
+                for (const r of rows) {
+                    if (r.tier === "doc" || r.tier === "raw" || r.tier === "reflection") {
+                        byTier[r.tier] = r.c;
+                    }
+                }
+                const newRows = db.db
+                    .prepare(`SELECT memory_tier AS tier, COUNT(*) AS c
+               FROM documents
+               WHERE date IS NOT NULL AND date >= @since
+               GROUP BY memory_tier`)
+                    .all({ since });
+                for (const r of newRows) {
+                    if (r.tier === "doc" || r.tier === "raw" || r.tier === "reflection") {
+                        newSince[r.tier] = r.c;
+                    }
+                }
+            }
+            else {
+                // v2 schema — everything treated as "doc"
+                byTier.doc = totalDocuments;
+                const newDocRow = db.db
+                    .prepare("SELECT COUNT(*) AS c FROM documents WHERE date IS NOT NULL AND date >= ?")
+                    .get(since);
+                newSince.doc = newDocRow.c;
+            }
+            let chunksPerDocP50 = 0;
+            let chunksPerDocP90 = 0;
+            if (hasChunks) {
+                const perDoc = db.db
+                    .prepare(`SELECT COUNT(*) AS c FROM chunks GROUP BY document_id`)
+                    .all();
+                const counts = perDoc.map((r) => r.c).sort((a, b) => a - b);
+                chunksPerDocP50 = percentile(counts, 0.5);
+                chunksPerDocP90 = percentile(counts, 0.9);
+            }
+            let lastReflectionAt = null;
+            if (hasTier) {
+                const row = db.db
+                    .prepare(`SELECT date FROM documents
+               WHERE memory_tier = 'reflection' AND date IS NOT NULL
+               ORDER BY date DESC LIMIT 1`)
+                    .get();
+                lastReflectionAt = row?.date ?? null;
+            }
+            const payload = {
+                total_documents: totalDocuments,
+                by_tier: byTier,
+                new_since: newSince,
+                chunks_per_doc_p50: chunksPerDocP50,
+                chunks_per_doc_p90: chunksPerDocP90,
+                last_reflection_at: lastReflectionAt,
+                since,
+            };
+            return { content: [{ type: "text", text: JSON.stringify(payload, null, 2) }] };
+        }
+        catch (e) {
+            return { content: [{ type: "text", text: `Error: ${e.message}` }], isError: true };
+        }
+    });
     server.tool("knowledge_record_outcome", "Record a pipeline outcome event (research, plan, phase, validation, etc.)", {
         event_type: z.string().describe("Event type (e.g., 'phase_completed', 'research_started')"),
         issue_number: z.number().describe("GitHub issue number"),

package/dist/index.js.map

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package/dist/llm-client.d.ts

@@ -0,0 +1,41 @@
+/**
+ * Minimal OpenAI-compatible LLM client for Contextual Retrieval.
+ *
+ * Probes `${baseUrl}/v1/models` for availability and calls
+ * `${baseUrl}/v1/chat/completions` to generate short context prefixes for
+ * document chunks. Uses native `fetch` + `AbortController` — no SDK dependency.
+ *
+ * Fail-open semantics: network errors, timeouts, non-200 responses, and
+ * malformed JSON all resolve without throwing. `available()` returns `false`;
+ * `contextualize()` returns an empty string. The caller is expected to treat
+ * an empty context prefix as "no context available" and continue.
+ *
+ * Defaults target `gemma-lab` at `http://localhost:8000` with the Gemma 4 26B
+ * MXFP8 model. Override via `RALPH_LLM_URL` / `RALPH_LLM_MODEL` env vars or
+ * explicit options.
+ */
+export interface LlmClientOptions {
+    /** Base URL for the OpenAI-compatible endpoint. Default: RALPH_LLM_URL env or http://localhost:8000. */
+    baseUrl?: string;
+    /** Model identifier sent in chat completion requests. Default: RALPH_LLM_MODEL env or mlx-community/gemma-4-26b-a4b-it-mxfp8. */
+    model?: string;
+    /** Timeout for contextualize() in milliseconds. Default: 30000. */
+    timeoutMs?: number;
+}
+export interface LlmClient {
+    /**
+     * Probe the endpoint for availability.
+     * Returns `true` iff `${baseUrl}/v1/models` responds with HTTP 200 within 2000ms.
+     * Returns `false` on timeout, connection refused, non-200, or any thrown exception.
+     */
+    available(): Promise<boolean>;
+    /**
+     * Generate a short (≤100 token) context prefix situating `chunkContent`
+     * within `fullDocument`, using the Anthropic Contextual Retrieval prompt.
+     *
+     * Returns the trimmed content string on success, or `""` on any error
+     * (network failure, timeout, non-2xx response, missing choices, malformed JSON).
+     */
+    contextualize(fullDocument: string, chunkContent: string): Promise<string>;
+}
+export declare function createLlmClient(opts?: LlmClientOptions): LlmClient;

package/dist/llm-client.js

@@ -0,0 +1,98 @@
+/**
+ * Minimal OpenAI-compatible LLM client for Contextual Retrieval.
+ *
+ * Probes `${baseUrl}/v1/models` for availability and calls
+ * `${baseUrl}/v1/chat/completions` to generate short context prefixes for
+ * document chunks. Uses native `fetch` + `AbortController` — no SDK dependency.
+ *
+ * Fail-open semantics: network errors, timeouts, non-200 responses, and
+ * malformed JSON all resolve without throwing. `available()` returns `false`;
+ * `contextualize()` returns an empty string. The caller is expected to treat
+ * an empty context prefix as "no context available" and continue.
+ *
+ * Defaults target `gemma-lab` at `http://localhost:8000` with the Gemma 4 26B
+ * MXFP8 model. Override via `RALPH_LLM_URL` / `RALPH_LLM_MODEL` env vars or
+ * explicit options.
+ */
+const DEFAULT_BASE_URL = "http://localhost:8000";
+const DEFAULT_MODEL = "mlx-community/gemma-4-26b-a4b-it-mxfp8";
+const DEFAULT_TIMEOUT_MS = 30000;
+const AVAILABLE_PROBE_TIMEOUT_MS = 2000;
+const MAX_CONTEXT_TOKENS = 120;
+/**
+ * Anthropic Contextual Retrieval prompt, verbatim from the parent plan Phase 2.
+ * Placeholders `{fullDocument}` and `{chunkContent}` are filled at call time.
+ */
+function buildContextualizePrompt(fullDocument, chunkContent) {
+    return `<document>
+${fullDocument}
+</document>
+
+Here is the chunk we want to situate within the whole document:
+
+<chunk>
+${chunkContent}
+</chunk>
+
+Please give a short succinct context to situate this chunk within the overall
+document for the purposes of improving search retrieval of the chunk. Answer only
+with the succinct context and nothing else.`;
+}
+export function createLlmClient(opts = {}) {
+    const baseUrl = opts.baseUrl ?? process.env.RALPH_LLM_URL ?? DEFAULT_BASE_URL;
+    const model = opts.model ?? process.env.RALPH_LLM_MODEL ?? DEFAULT_MODEL;
+    const timeoutMs = opts.timeoutMs ?? DEFAULT_TIMEOUT_MS;
+    async function available() {
+        const controller = new AbortController();
+        const timer = setTimeout(() => controller.abort(), AVAILABLE_PROBE_TIMEOUT_MS);
+        try {
+            const response = await fetch(`${baseUrl}/v1/models`, {
+                method: "GET",
+                signal: controller.signal,
+            });
+            return response.status === 200;
+        }
+        catch {
+            return false;
+        }
+        finally {
+            clearTimeout(timer);
+        }
+    }
+    async function contextualize(fullDocument, chunkContent) {
+        const controller = new AbortController();
+        const timer = setTimeout(() => controller.abort(), timeoutMs);
+        try {
+            const prompt = buildContextualizePrompt(fullDocument, chunkContent);
+            const response = await fetch(`${baseUrl}/v1/chat/completions`, {
+                method: "POST",
+                headers: {
+                    "Content-Type": "application/json",
+                },
+                body: JSON.stringify({
+                    model,
+                    messages: [{ role: "user", content: prompt }],
+                    max_tokens: MAX_CONTEXT_TOKENS,
+                }),
+                signal: controller.signal,
+            });
+            if (!response.ok) {
+                return "";
+            }
+            const data = (await response.json());
+            const content = data?.choices?.[0]?.message?.content;
+            if (typeof content !== "string") {
+                return "";
+            }
+            return content.trim();
+        }
+        catch {
+            return "";
+        }
+        finally {
+            clearTimeout(timer);
+        }
+    }
+    return { available, contextualize };
+}
+//# sourceMappingURL=llm-client.js.map

package/dist/llm-client.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"llm-client.js","sourceRoot":"","sources":["../src/llm-client.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;GAeG;AA6BH,MAAM,gBAAgB,GAAG,uBAAuB,CAAC;AACjD,MAAM,aAAa,GAAG,wCAAwC,CAAC;AAC/D,MAAM,kBAAkB,GAAG,KAAK,CAAC;AACjC,MAAM,0BAA0B,GAAG,IAAI,CAAC;AACxC,MAAM,kBAAkB,GAAG,GAAG,CAAC;AAE/B;;;GAGG;AACH,SAAS,wBAAwB,CAAC,YAAoB,EAAE,YAAoB;IAC1E,OAAO;EACP,YAAY;;;;;;EAMZ,YAAY;;;;;4CAK8B,CAAC;AAC7C,CAAC;AAUD,MAAM,UAAU,eAAe,CAAC,OAAyB,EAAE;IACzD,MAAM,OAAO,GAAG,IAAI,CAAC,OAAO,IAAI,OAAO,CAAC,GAAG,CAAC,aAAa,IAAI,gBAAgB,CAAC;IAC9E,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,IAAI,OAAO,CAAC,GAAG,CAAC,eAAe,IAAI,aAAa,CAAC;IACzE,MAAM,SAAS,GAAG,IAAI,CAAC,SAAS,IAAI,kBAAkB,CAAC;IAEvD,KAAK,UAAU,SAAS;QACtB,MAAM,UAAU,GAAG,IAAI,eAAe,EAAE,CAAC;QACzC,MAAM,KAAK,GAAG,UAAU,CAAC,GAAG,EAAE,CAAC,UAAU,CAAC,KAAK,EAAE,EAAE,0BAA0B,CAAC,CAAC;QAC/E,IAAI,CAAC;YACH,MAAM,QAAQ,GAAG,MAAM,KAAK,CAAC,GAAG,OAAO,YAAY,EAAE;gBACnD,MAAM,EAAE,KAAK;gBACb,MAAM,EAAE,UAAU,CAAC,MAAM;aAC1B,CAAC,CAAC;YACH,OAAO,QAAQ,CAAC,MAAM,KAAK,GAAG,CAAC;QACjC,CAAC;QAAC,MAAM,CAAC;YACP,OAAO,KAAK,CAAC;QACf,CAAC;gBAAS,CAAC;YACT,YAAY,CAAC,KAAK,CAAC,CAAC;QACtB,CAAC;IACH,CAAC;IAED,KAAK,UAAU,aAAa,CAAC,YAAoB,EAAE,YAAoB;QACrE,MAAM,UAAU,GAAG,IAAI,eAAe,EAAE,CAAC;QACzC,MAAM,KAAK,GAAG,UAAU,CAAC,GAAG,EAAE,CAAC,UAAU,CAAC,KAAK,EAAE,EAAE,SAAS,CAAC,CAAC;QAC9D,IAAI,CAAC;YACH,MAAM,MAAM,GAAG,wBAAwB,CAAC,YAAY,EAAE,YAAY,CAAC,CAAC;YACpE,MAAM,QAAQ,GAAG,MAAM,KAAK,CAAC,GAAG,OAAO,sBAAsB,EAAE;gBAC7D,MAAM,EAAE,MAAM;gBACd,OAAO,EAAE;oBACP,cAAc,EAAE,kBAAkB;iBACnC;gBACD,IAAI,EAAE,IAAI,CAAC,SAAS,CAAC;oBACnB,KAAK;oBACL,QAAQ,EAAE,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,OAAO,EAAE,MAAM,EAAE,CAAC;oBAC7C,UAAU,EAAE,kBAAkB;iBAC/B,CAAC;gBACF,MAAM,EAAE,UAAU,CAAC,MAAM;aAC1B,CAAC,CAAC;YAEH,IAAI,CAAC,QAAQ,CAAC,EAAE,EAAE,CAAC;gBACjB,OAAO,EAAE,CAAC;YACZ,CAAC;YAED,MAAM,IAAI,GAAG,CAAC,MAAM,QAAQ,CAAC,IAAI,EAAE,CAA2B,CAAC;YAC/D,MAAM,OAAO,GAAG,IAAI,EAAE,OAAO,EAAE,CAAC,CAAC,CAAC,EAAE,OAAO,EAAE,OAAO,CAAC;YACrD,IAAI,OAAO,OAAO,KAAK,QAAQ,EAAE,CAAC;gBAChC,OAAO,EAAE,CAAC;YACZ,CAAC;YACD,OAAO,OAAO,CAAC,IAAI,EAAE,CAAC;QACxB,CAAC;QAAC,MAAM,CAAC;YACP,OAAO,EAAE,CAAC;QACZ,CAAC;gBAAS,CAAC;YACT,YAAY,CAAC,KAAK,CAAC,CAAC;QACtB,CAAC;IACH,CAAC;IAED,OAAO,EAAE,SAAS,EAAE,aAAa,EAAE,CAAC;AACtC,CAAC"}

package/dist/reindex.d.ts

@@ -1,6 +1,25 @@
-export declare function reindex(dirs: string[], dbPath: string, generate?: boolean): Promise<void>;
-export declare function resolveDirs(): {
+import { type KnowledgeConfig } from "./config.js";
+export declare function reindex(dirs: string[], dbPath: string, generate?: boolean, ignorePatterns?: string[]): Promise<void>;
+export type ResolvedDirsSource = "cli" | "env" | "config" | "fallback";
+export interface ResolvedDirs {
     dirs: string[];
     dbPath: string;
     generate: boolean;
-};
+    source: ResolvedDirsSource;
+    config: KnowledgeConfig;
+}
+/**
+ * Resolve the set of roots, database path, and generate flag for a reindex
+ * run. Precedence (highest to lowest):
+ *   1. CLI positional args
+ *   2. `RALPH_KNOWLEDGE_DIRS` environment variable
+ *   3. `config.roots` from `~/.ralph/knowledge.config.json`
+ *   4. `"../../thoughts"` fallback
+ *
+ * `dbPath` precedence is independent: CLI `.db` positional > `RALPH_KNOWLEDGE_DB`
+ * env var > `config.dbPath` > {@link DEFAULT_DB_PATH}.
+ *
+ * The returned `config` is forwarded to the caller so `ignorePatterns` can be
+ * threaded into {@link reindex}.
+ */
+export declare function resolveDirs(): ResolvedDirs;

package/dist/reindex.js

@@ -8,7 +8,9 @@ import { embed, prepareTextForEmbedding } from "./embedder.js";
 import { parseDocument } from "./parser.js";
 import { findMarkdownFiles } from "./file-scanner.js";
 import { generateIndexes } from "./generate-indexes.js";
-export async function reindex(dirs, dbPath, generate = false) {
+import { loadConfig } from "./config.js";
+import { loadIgnoreForRoot } from "./ignore.js";
+export async function reindex(dirs, dbPath, generate = false, ignorePatterns) {
     console.log(`Indexing ${dirs.join(", ")} -> ${dbPath}`);
     const db = new KnowledgeDB(dbPath);
     const fts = new FtsSearch(db);
@@ -28,7 +30,8 @@ export async function reindex(dirs, dbPath, generate = false) {
     // Phase 1: Discover files on disk
     const filesOnDisk = [];
     for (const dir of dirs) {
-        const found = findMarkdownFiles(dir);
+        const matcher = loadIgnoreForRoot(dir, ignorePatterns);
+        const found = findMarkdownFiles(dir, matcher);
         console.log(`  ${dir}: ${found.length} files`);
         filesOnDisk.push(...found);
     }
@@ -158,28 +161,77 @@ export async function reindex(dirs, dbPath, generate = false) {
     }
 }
 const DEFAULT_DB_PATH = join(homedir(), ".ralph-hero", "knowledge.db");
+/**
+ * Resolve the set of roots, database path, and generate flag for a reindex
+ * run. Precedence (highest to lowest):
+ *   1. CLI positional args
+ *   2. `RALPH_KNOWLEDGE_DIRS` environment variable
+ *   3. `config.roots` from `~/.ralph/knowledge.config.json`
+ *   4. `"../../thoughts"` fallback
+ *
+ * `dbPath` precedence is independent: CLI `.db` positional > `RALPH_KNOWLEDGE_DB`
+ * env var > `config.dbPath` > {@link DEFAULT_DB_PATH}.
+ *
+ * The returned `config` is forwarded to the caller so `ignorePatterns` can be
+ * threaded into {@link reindex}.
+ */
 export function resolveDirs() {
     const cliArgs = process.argv.slice(2);
     const noGenerate = cliArgs.includes("--no-generate");
     const positional = cliArgs.filter(a => !a.startsWith("--"));
     const cliDb = positional.find(a => a.endsWith(".db"));
     const cliDirs = positional.filter(a => !a.endsWith(".db"));
+    const config = loadConfig();
+    const resolveDbPath = () => cliDb ??
+        process.env.RALPH_KNOWLEDGE_DB ??
+        config.dbPath ??
+        DEFAULT_DB_PATH;
     if (cliDirs.length > 0) {
-        return { dirs: cliDirs, dbPath: cliDb ?? DEFAULT_DB_PATH, generate: !noGenerate };
+        console.log("Using roots from: CLI");
+        return {
+            dirs: cliDirs,
+            dbPath: resolveDbPath(),
+            generate: !noGenerate,
+            source: "cli",
+            config,
+        };
     }
     const envDirs = process.env.RALPH_KNOWLEDGE_DIRS;
     if (envDirs) {
+        const parsed = envDirs.split(",").map(d => d.trim()).filter(Boolean);
+        if (parsed.length > 0) {
+            console.log("Using roots from: env");
+            return {
+                dirs: parsed,
+                dbPath: resolveDbPath(),
+                generate: !noGenerate,
+                source: "env",
+                config,
+            };
+        }
+    }
+    if (config.roots && config.roots.length > 0) {
+        console.log("Using roots from: config");
         return {
-            dirs: envDirs.split(",").map(d => d.trim()).filter(Boolean),
-            dbPath: cliDb ?? process.env.RALPH_KNOWLEDGE_DB ?? DEFAULT_DB_PATH,
+            dirs: config.roots,
+            dbPath: resolveDbPath(),
             generate: !noGenerate,
+            source: "config",
+            config,
         };
     }
-    return { dirs: ["../../thoughts"], dbPath: cliDb ?? DEFAULT_DB_PATH, generate: !noGenerate };
+    console.log("Using roots from: fallback");
+    return {
+        dirs: ["../../thoughts"],
+        dbPath: resolveDbPath(),
+        generate: !noGenerate,
+        source: "fallback",
+        config,
+    };
 }
 const isMain = process.argv[1]?.endsWith("reindex.js");
 if (isMain) {
-    const { dirs, dbPath, generate } = resolveDirs();
-    reindex(dirs, dbPath, generate).catch(console.error);
+    const { dirs, dbPath, generate, config } = resolveDirs();
+    reindex(dirs, dbPath, generate, config.ignorePatterns).catch(console.error);
 }
 //# sourceMappingURL=reindex.js.map

package/dist/reindex.js.map

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+{"version":3,"file":"reindex.js","sourceRoot":"","sources":["../src/reindex.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,YAAY,EAAE,QAAQ,EAAE,MAAM,SAAS,CAAC;AACjD,OAAO,EAAE,IAAI,EAAE,QAAQ,EAAE,OAAO,EAAE,QAAQ,EAAE,MAAM,WAAW,CAAC;AAC9D,OAAO,EAAE,OAAO,EAAE,MAAM,SAAS,CAAC;AAClC,OAAO,EAAE,WAAW,EAAE,MAAM,SAAS,CAAC;AACtC,OAAO,EAAE,SAAS,EAAE,MAAM,aAAa,CAAC;AACxC,OAAO,EAAE,YAAY,EAAE,MAAM,oBAAoB,CAAC;AAClD,OAAO,EAAE,KAAK,EAAE,uBAAuB,EAAE,MAAM,eAAe,CAAC;AAC/D,OAAO,EAAE,aAAa,EAAuB,MAAM,aAAa,CAAC;AACjE,OAAO,EAAE,iBAAiB,EAAE,MAAM,mBAAmB,CAAC;AACtD,OAAO,EAAE,eAAe,EAAE,MAAM,uBAAuB,CAAC;AACxD,OAAO,EAAE,UAAU,EAAwB,MAAM,aAAa,CAAC;AAC/D,OAAO,EAAE,iBAAiB,EAAE,MAAM,aAAa,CAAC;AAEhD,MAAM,CAAC,KAAK,UAAU,OAAO,CAC3B,IAAc,EACd,MAAc,EACd,WAAoB,KAAK,EACzB,cAAyB;IAEzB,OAAO,CAAC,GAAG,CAAC,YAAY,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,OAAO,MAAM,EAAE,CAAC,CAAC;IAExD,MAAM,EAAE,GAAG,IAAI,WAAW,CAAC,MAAM,CAAC,CAAC;IACnC,MAAM,GAAG,GAAG,IAAI,SAAS,CAAC,EAAE,CAAC,CAAC;IAC9B,GAAG,CAAC,WAAW,EAAE,CAAC;IAClB,MAAM,GAAG,GAAG,IAAI,YAAY,CAAC,EAAE,CAAC,CAAC;IACjC,GAAG,CAAC,WAAW,EAAE,CAAC;IAElB,8EAA8E;IAC9E,MAAM,cAAc,GAAG,GAAG,CAAC;IAC3B,MAAM,cAAc,GAAG,EAAE,CAAC,OAAO,CAAC,gBAAgB,CAAC,CAAC;IACpD,IAAI,mBAAmB,GAAG,KAAK,CAAC;IAChC,IAAI,cAAc,KAAK,cAAc,EAAE,CAAC;QACtC,OAAO,CAAC,GAAG,CAAC,uEAAuE,CAAC,CAAC;QACrF,EAAE,CAAC,gBAAgB,EAAE,CAAC;QACtB,EAAE,CAAC,OAAO,CAAC,gBAAgB,EAAE,cAAc,CAAC,CAAC;QAC7C,mBAAmB,GAAG,IAAI,CAAC;IAC7B,CAAC;IAED,kCAAkC;IAClC,MAAM,WAAW,GAAa,EAAE,CAAC;IACjC,KAAK,MAAM,GAAG,IAAI,IAAI,EAAE,CAAC;QACvB,MAAM,OAAO,GAAG,iBAAiB,CAAC,GAAG,EAAE,cAAc,CAAC,CAAC;QACvD,MAAM,KAAK,GAAG,iBAAiB,CAAC,GAAG,EAAE,OAAO,CAAC,CAAC;QAC9C,OAAO,CAAC,GAAG,CAAC,KAAK,GAAG,KAAK,KAAK,CAAC,MAAM,QAAQ,CAAC,CAAC;QAC/C,WAAW,CAAC,IAAI,CAAC,GAAG,KAAK,CAAC,CAAC;IAC7B,CAAC;IACD,OAAO,CAAC,GAAG,CAAC,SAAS,WAAW,CAAC,MAAM,uBAAuB,CAAC,CAAC;IAEhE,MAAM,cAAc,GAAG,IAAI,GAAG,CAAC,WAAW,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;IAEjE,4DAA4D;IAC5D,MAAM,WAAW,GAAG,EAAE,CAAC,eAAe,EAAE,CAAC;IACzC,IAAI,OAAO,GAAG,CAAC,CAAC;IAChB,KAAK,MAAM,UAAU,IAAI,WAAW,EAAE,CAAC;QACrC,IAAI,CAAC,cAAc,CAAC,GAAG,CAAC,UAAU,CAAC,EAAE,CAAC;YACpC,MAAM,EAAE,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,CAAC,CAAC;YACvC,GAAG,CAAC,cAAc,CAAC,EAAE,CAAC,CAAC;YACvB,EAAE,CAAC,cAAc,CAAC,EAAE,CAAC,CAAC;YACtB,GAAG,CAAC,eAAe,CAAC,EAAE,CAAC,CAAC;YACxB,EAAE,CAAC,gBAAgB,CAAC,UAAU,CAAC,CAAC;YAChC,OAAO,EAAE,CAAC;QACZ,CAAC;IACH,CAAC;IACD,IAAI,OAAO,GAAG,CAAC,EAAE,CAAC;QAChB,OAAO,CAAC,GAAG,CAAC,aAAa,OAAO,gBAAgB,CAAC,CAAC;IACpD,CAAC;IAED,yCAAyC;IACzC,MAAM,UAAU,GAAqB,EAAE,CAAC;IACxC,IAAI,OAAO,GAAG,CAAC,CAAC;IAChB,IAAI,OAAO,GAAG,CAAC,CAAC;IAChB,KAAK,MAAM,QAAQ,IAAI,WAAW,EAAE,CAAC;QACnC,MAAM,OAAO,GAAG,OAAO,CAAC,QAAQ,CAAC,CAAC;QAClC,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,QAAQ,CAAC,OAAO,CAAC,CAAC,OAAO,CAAC,CAAC;QAEpD,8CAA8C;QAC9C,MAAM,UAAU,GAAG,EAAE,CAAC,aAAa,CAAC,OAAO,CAAC,CAAC;QAC7C,IAAI,UAAU,IAAI,UAAU,CAAC,KAAK,KAAK,KAAK,EAAE,CAAC;YAC7C,OAAO,EAAE,CAAC;YACV,SAAS;QACX,CAAC;QAED,MAAM,GAAG,GAAG,YAAY,CAAC,QAAQ,EAAE,OAAO,CAAC,CAAC;QAC5C,MAAM,SAAS,GAAG,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,OAAO,CAAC,UAAU,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;QACjE,MAAM,OAAO,GAAG,SAAS;YACvB,CAAC,CAAC,QAAQ,CAAC,OAAO,CAAC,SAAS,EAAE,IAAI,CAAC,EAAE,OAAO,CAAC;YAC7C,CAAC,CAAC,QAAQ,CAAC;QACb,MAAM,EAAE,GAAG,QAAQ,CAAC,QAAQ,EAAE,KAAK,CAAC,CAAC;QAErC,MAAM,MAAM,GAAG,aAAa,CAAC,EAAE,EAAE,OAAO,EAAE,GAAG,CAAC,CAAC;QAC/C,UAAU,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;QAExB,MAAM,OAAO,GAAa,EAAE,CAAC;QAC7B,IAAI,CAAC,MAAM,CAAC,IAAI;YAAE,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;QACvC,IAAI,CAAC,MAAM,CAAC,IAAI;YAAE,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;QACvC,IAAI,CAAC,MAAM,CAAC,MAAM;YAAE,OAAO,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC;QAC3C,IAAI,OAAO,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YACvB,OAAO,CAAC,IAAI,CAAC,cAAc,EAAE,yBAAyB,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAC9E,CAAC;QAED,uEAAuE;QACvE,IAAI,EAAE,CAAC,cAAc,CAAC,MAAM,CAAC,EAAE,CAAC,EAAE,CAAC;YACjC,GAAG,CAAC,cAAc,CAAC,MAAM,CAAC,EAAE,CAAC,CAAC;QAChC,CAAC;QAED,EAAE,CAAC,cAAc,CAAC;YAChB,EAAE,EAAE,MAAM,CAAC,EAAE;YACb,IAAI,EAAE,MAAM,CAAC,IAAI;YACjB,KAAK,EAAE,MAAM,CAAC,KAAK;YACnB,IAAI,EAAE,MAAM,CAAC,IAAI;YACjB,IAAI,EAAE,MAAM,CAAC,IAAI;YACjB,MAAM,EAAE,MAAM,CAAC,MAAM;YACrB,WAAW,EAAE,MAAM,CAAC,WAAW;YAC/B,OAAO,EAAE,MAAM,CAAC,OAAO;SACxB,CAAC,CAAC;QAEH,oCAAoC;QACpC,GAAG,CAAC,cAAc,CAAC,MAAM,CAAC,EAAE,CAAC,CAAC;QAE9B,IAAI,MAAM,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YAC3B,EAAE,CAAC,OAAO,CAAC,MAAM,CAAC,EAAE,EAAE,MAAM,CAAC,IAAI,CAAC,CAAC;QACrC,CAAC;QAED,4EAA4E;QAC5E,EAAE,CAAC,EAAE,CAAC,OAAO,CAAC,+CAA+C,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,CAAC,CAAC;QAE9E,6EAA6E;QAC7E,gFAAgF;QAChF,8EAA8E;QAC9E,8CAA8C;QAC9C,KAAK,MAAM,GAAG,IAAI,MAAM,CAAC,aAAa,EAAE,CAAC;YACvC,EAAE,CAAC,kBAAkB,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC;YACpC,EAAE,CAAC,eAAe,CAAC,GAAG,CAAC,QAAQ,EAAE,GAAG,CAAC,QAAQ,EAAE,GAAG,CAAC,IAAI,CAAC,CAAC;QAC3D,CAAC;QAED,KAAK,MAAM,IAAI,IAAI,MAAM,CAAC,YAAY,EAAE,CAAC;YACvC,EAAE,CAAC,kBAAkB,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC;YACrC,EAAE,CAAC,eAAe,CAAC,IAAI,CAAC,QAAQ,EAAE,IAAI,CAAC,QAAQ,EAAE,SAAS,EAAE,IAAI,CAAC,OAAO,CAAC,CAAC;QAC5E,CAAC;QAED,MAAM,IAAI,GAAG,uBAAuB,CAAC,MAAM,CAAC,KAAK,EAAE,MAAM,CAAC,IAAI,EAAE,MAAM,CAAC,OAAO,C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package/dist/search.d.ts

@@ -1,9 +1,11 @@
 import type { KnowledgeDB } from "./db.js";
+export type MemoryTier = "doc" | "raw" | "reflection" | "any";
 export interface SearchOptions {
     type?: string;
     tags?: string[];
     includeSuperseded?: boolean;
     limit?: number;
+    memoryTier?: MemoryTier;
 }
 export interface SearchResult {
     id: string;
@@ -14,6 +16,11 @@ export interface SearchResult {
     date: string | null;
     score: number;
     snippet: string;
+    chunkIndex?: number;
+    charStart?: number;
+    charEnd?: number;
+    contextPrefix?: string;
+    bestChunkId?: string;
 }
 export declare class FtsSearch {
     private readonly db;
@@ -37,5 +44,10 @@ export declare class FtsSearch {
     ensureTable(): void;
     rebuildIndex(): void;
     private escapeFts5Query;
+    /**
+     * Returns true when the `documents.memory_tier` column exists (schema v3+).
+     * On v2 schemas this is false and the memoryTier filter is silently ignored.
+     */
+    private memoryTierColumnExists;
     search(query: string, options?: SearchOptions): SearchResult[];
 }