ralph-hero-knowledge-index 0.1.7 → 0.1.10

package/.claude-plugin/plugin.json

@@ -1,6 +1,6 @@
 {
   "name": "ralph-knowledge",
-  "version": "0.1.7",
+  "version": "0.1.10",
   "description": "Knowledge graph for ralph-hero: semantic search, relationship traversal, and document indexing across thoughts/ documents. Optional companion to ralph-hero.",
   "author": {
     "name": "Chad Dubiel",

package/.mcp.json

@@ -2,7 +2,7 @@
   "mcpServers": {
     "ralph-knowledge": {
       "command": "npx",
-      "args": ["-y", "ralph-hero-knowledge-index@0.1.7"]
+      "args": ["-y", "ralph-hero-knowledge-index@0.1.10"]
     }
   }
 }

package/dist/parser.js

@@ -32,7 +32,13 @@ export function parseDocument(id, path, raw) {
         date: frontmatter.date ? String(frontmatter.date) : null,
         type: frontmatter.type ?? null,
         status: frontmatter.status ?? null,
-        githubIssue: typeof frontmatter.github_issue === "number" ? frontmatter.github_issue : null,
+        githubIssue: typeof frontmatter.github_issue === "number"
+            ? frontmatter.github_issue
+            : Array.isArray(frontmatter.github_issues) && typeof frontmatter.github_issues[0] === "number"
+                ? frontmatter.github_issues[0]
+                : typeof frontmatter.primary_issue === "number"
+                    ? frontmatter.primary_issue
+                    : null,
         tags, relationships, content: body,
     };
 }

package/dist/parser.js.map

@@ -1 +1 @@
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+{"version":3,"file":"parser.js","sourceRoot":"","sources":["../src/parser.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,IAAI,SAAS,EAAE,MAAM,MAAM,CAAC;AAqB1C,MAAM,cAAc,GAAG,uBAAuB,CAAC;AAC/C,MAAM,QAAQ,GAAG,WAAW,CAAC;AAC7B,MAAM,eAAe,GAAG,2CAA2C,CAAC;AACpE,MAAM,gBAAgB,GAAG,eAAe,CAAC;AAEzC,MAAM,UAAU,aAAa,CAAC,EAAU,EAAE,IAAY,EAAE,GAAW;IACjE,MAAM,OAAO,GAAG,GAAG,CAAC,KAAK,CAAC,cAAc,CAAC,CAAC;IAC1C,MAAM,WAAW,GAAG,OAAO,CAAC,CAAC,CAAC,SAAS,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;IAC/D,MAAM,IAAI,GAAG,OAAO,CAAC,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,IAAI,EAAE,CAAC;IACxE,MAAM,UAAU,GAAG,IAAI,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAC;IACxC,MAAM,KAAK,GAAG,UAAU,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;IAErD,MAAM,aAAa,GAAmB,EAAE,CAAC;IACzC,IAAI,KAA6B,CAAC;IAClC,MAAM,KAAK,GAAG,IAAI,MAAM,CAAC,eAAe,CAAC,MAAM,EAAE,IAAI,CAAC,CAAC;IACvD,OAAO,CAAC,KAAK,GAAG,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,KAAK,IAAI,EAAE,CAAC;QAC3C,aAAa,CAAC,IAAI,CAAC;YACjB,QAAQ,EAAE,EAAE;YACZ,QAAQ,EAAE,KAAK,CAAC,CAAC,CAAC;YAClB,IAAI,EAAE,KAAK,CAAC,CAAC,CAA6B;SAC3C,CAAC,CAAC;IACL,CAAC;IAED,MAAM,YAAY,GAAG,WAAW,CAAC,aAAa,CAAC;IAC/C,IAAI,OAAO,YAAY,KAAK,QAAQ,EAAE,CAAC;QACrC,MAAM,OAAO,GAAG,YAAY,CAAC,KAAK,CAAC,gBAAgB,CAAC,CAAC;QACrD,IAAI,OAAO,EAAE,CAAC;YACZ,aAAa,CAAC,IAAI,CAAC,EAAE,QAAQ,EAAE,EAAE,EAAE,QAAQ,EAAE,OAAO,CAAC,CAAC,CAAC,EAAE,IAAI,EAAE,eAAe,EAAE,CAAC,CAAC;QACpF,CAAC;IACH,CAAC;IAED,MAAM,IAAI,GAAa,KAAK,CAAC,OAAO,CAAC,WAAW,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,WAAW,CAAC,IAAI,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;IAE3F,OAAO;QACL,EAAE,EAAE,IAAI,EAAE,KAAK;QACf,IAAI,EAAE,WAAW,CAAC,IAAI,CAAC,CAAC,CAAC,MAAM,CAAC,WAAW,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,IAAI;QACxD,IAAI,EAAE,WAAW,CAAC,IAAI,IAAI,IAAI;QAC9B,MAAM,EAAE,WAAW,CAAC,MAAM,IAAI,IAAI;QAClC,WAAW,EAAE,OAAO,WAAW,CAAC,YAAY,KAAK,QAAQ;YACvD,CAAC,CAAC,WAAW,CAAC,YAAY;YAC1B,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,WAAW,CAAC,aAAa,CAAC,IAAI,OAAO,WAAW,CAAC,aAAa,CAAC,CAAC,CAAC,KAAK,QAAQ;gBAC5F,CAAC,CAAC,WAAW,CAAC,aAAa,CAAC,CAAC,CAAC;gBAC9B,CAAC,CAAC,OAAO,WAAW,CAAC,aAAa,KAAK,QAAQ;oBAC7C,CAAC,CAAC,WAAW,CAAC,aAAa;oBAC3B,CAAC,CAAC,IAAI;QACZ,IAAI,EAAE,aAAa,EAAE,OAAO,EAAE,IAAI;KACnC,CAAC;AACJ,CAAC"}

package/dist/reindex.d.ts

@@ -1 +1,6 @@
-export {};
+export declare function findMarkdownFiles(dir: string): string[];
+export declare function reindex(dirs: string[], dbPath: string): Promise<void>;
+export declare function resolveDirs(): {
+    dirs: string[];
+    dbPath: string;
+};

package/dist/reindex.js

@@ -1,12 +1,12 @@
 import { readFileSync, readdirSync } from "node:fs";
-import { join, relative, basename } from "node:path";
+import { join, relative, resolve, basename } from "node:path";
 import { homedir } from "node:os";
 import { KnowledgeDB } from "./db.js";
 import { FtsSearch } from "./search.js";
 import { VectorSearch } from "./vector-search.js";
 import { embed, prepareTextForEmbedding } from "./embedder.js";
 import { parseDocument } from "./parser.js";
-function findMarkdownFiles(dir) {
+export function findMarkdownFiles(dir) {
     const results = [];
     function walk(d) {
         for (const entry of readdirSync(d, { withFileTypes: true })) {
@@ -22,8 +22,8 @@ function findMarkdownFiles(dir) {
     walk(dir);
     return results;
 }
-async function reindex(thoughtsDir, dbPath) {
-    console.log(`Indexing ${thoughtsDir} -> ${dbPath}`);
+export async function reindex(dirs, dbPath) {
+    console.log(`Indexing ${dirs.join(", ")} -> ${dbPath}`);
     const db = new KnowledgeDB(dbPath);
     const fts = new FtsSearch(db);
     const vec = new VectorSearch(db);
@@ -31,12 +31,21 @@ async function reindex(thoughtsDir, dbPath) {
     db.clearAll();
     vec.dropIndex();
     vec.createIndex();
-    const files = findMarkdownFiles(thoughtsDir);
-    console.log(`Found ${files.length} markdown files`);
+    const files = [];
+    for (const dir of dirs) {
+        const found = findMarkdownFiles(dir);
+        console.log(`  ${dir}: ${found.length} files`);
+        files.push(...found);
+    }
+    console.log(`Found ${files.length} total markdown files`);
     let indexed = 0;
     for (const filePath of files) {
         const raw = readFileSync(filePath, "utf-8");
-        const relPath = relative(join(thoughtsDir, ".."), filePath);
+        const absPath = resolve(filePath);
+        const sourceDir = dirs.find(d => absPath.startsWith(resolve(d)));
+        const relPath = sourceDir
+            ? relative(resolve(sourceDir, ".."), absPath)
+            : filePath;
         const id = basename(filePath, ".md");
         const parsed = parseDocument(id, relPath, raw);
         db.upsertDocument({
@@ -73,7 +82,25 @@ async function reindex(thoughtsDir, dbPath) {
     db.close();
 }
 const DEFAULT_DB_PATH = join(homedir(), ".ralph-hero", "knowledge.db");
-const thoughtsDir = process.argv[2] ?? "../../thoughts";
-const dbPath = process.argv[3] ?? DEFAULT_DB_PATH;
-reindex(thoughtsDir, dbPath).catch(console.error);
+export function resolveDirs() {
+    const cliArgs = process.argv.slice(2);
+    const cliDb = cliArgs.find(a => a.endsWith(".db"));
+    const cliDirs = cliArgs.filter(a => !a.endsWith(".db"));
+    if (cliDirs.length > 0) {
+        return { dirs: cliDirs, dbPath: cliDb ?? DEFAULT_DB_PATH };
+    }
+    const envDirs = process.env.RALPH_KNOWLEDGE_DIRS;
+    if (envDirs) {
+        return {
+            dirs: envDirs.split(",").map(d => d.trim()).filter(Boolean),
+            dbPath: cliDb ?? process.env.RALPH_KNOWLEDGE_DB ?? DEFAULT_DB_PATH,
+        };
+    }
+    return { dirs: ["../../thoughts"], dbPath: cliDb ?? DEFAULT_DB_PATH };
+}
+const isMain = process.argv[1]?.endsWith("reindex.js");
+if (isMain) {
+    const { dirs, dbPath } = resolveDirs();
+    reindex(dirs, dbPath).catch(console.error);
+}
 //# sourceMappingURL=reindex.js.map

package/dist/reindex.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "ralph-hero-knowledge-index",
-  "version": "0.1.7",
+  "version": "0.1.10",
   "type": "module",
   "main": "dist/index.js",
   "bin": {

package/skills/setup/SKILL.md

@@ -1,11 +1,11 @@
 ---
 description: Set up or rebuild the ralph-knowledge index from markdown documents. Use when setting up ralph-knowledge for the first time, reindexing after adding new documents, rebuilding a corrupted knowledge DB, or when knowledge_search returns empty results. Also use when the user mentions "index thoughts", "reindex", "set up knowledge", or "knowledge search not working".
-argument-hint: "[thoughts-directory]"
+argument-hint: "[directory1,directory2,...]"
 ---
 
 # Ralph Knowledge Setup
 
-Interactive setup and reindex skill for the ralph-knowledge plugin. Indexes markdown documents from a `thoughts/` directory into a SQLite database with full-text search and semantic embeddings.
+Interactive setup and reindex skill for the ralph-knowledge plugin. Indexes markdown documents from one or more directories into a SQLite database with full-text search and semantic embeddings.
 
 ## Prerequisites
 
@@ -41,6 +41,36 @@ Proceed with indexing?
 
 If not found, ask the user for the path.
 
+### Step 1b: Additional directories
+
+After confirming the thoughts directory, check if `RALPH_KNOWLEDGE_DIRS` is set in the environment. If it contains additional directories beyond the one found in Step 1, note them:
+
+```
+Also indexing from RALPH_KNOWLEDGE_DIRS: docs/plans, docs/adr
+```
+
+If `RALPH_KNOWLEDGE_DIRS` is NOT set, ask:
+
+```
+Would you like to index additional directories alongside thoughts/?
+Common choices: docs/, docs/plans/, docs/adr/
+
+Enter comma-separated paths (relative to project root), or press Enter to skip:
+```
+
+If the user provides additional directories, validate each exists. Combine all directories into a single list for Step 3.
+
+If the user wants to persist this, suggest:
+
+```
+To persist, add to .claude/settings.local.json:
+{
+  "env": {
+    "RALPH_KNOWLEDGE_DIRS": "thoughts,docs/plans"
+  }
+}
+```
+
 ### Step 2: Determine the DB path
 
 The default DB path is `~/.ralph-hero/knowledge.db`. The directory is auto-created if it doesn't exist.
@@ -55,9 +85,11 @@ The reindex script is bundled in the npm package. Install it to a temp location
 
 ```bash
 cd /tmp && npm install --no-save ralph-hero-knowledge-index@latest 2>&1 | tail -3
-node /tmp/node_modules/ralph-hero-knowledge-index/dist/reindex.js [thoughts-dir] [db-path]
+node /tmp/node_modules/ralph-hero-knowledge-index/dist/reindex.js [dir1] [dir2] ... [db-path]
 ```
 
+Pass all directories as separate arguments, followed by the database path (ending in `.db`).
+
 Display the output as it runs. The script will:
 - Scan for all `.md` files recursively (skipping dot-directories)
 - Parse frontmatter (title, date, type, status, tags)
@@ -89,12 +121,14 @@ Knowledge Index Ready
 =====================
 Documents indexed: [N]
 Database: [db-path]
-Thoughts directory: [thoughts-dir]
+Directories indexed:
+  - thoughts/
+  - docs/plans/
 
 Tools available:
   - knowledge_search: Keyword + semantic search across documents
   - knowledge_traverse: Walk relationship edges between documents
 
 To reindex after adding new documents:
-  /ralph-knowledge:setup [thoughts-dir]
+  /ralph-knowledge:setup
 ```

package/skills/setup-workspace/iteration-1/eval-first-time-setup/with_skill/outputs/output.md

@@ -0,0 +1,88 @@
+# Ralph Knowledge Setup
+
+## Step 1: Locate the thoughts directory
+
+Found thoughts directory: `./thoughts/` (`/home/chad_a_dubiel/projects/ralph-hero/thoughts/`)
+Contains **454** markdown files.
+
+Proceed with indexing? **yes**
+
+## Step 2: Determine the DB path
+
+`RALPH_KNOWLEDGE_DB` is not set in the environment.
+
+Defaulting to `knowledge.db` in the project root: `/home/chad_a_dubiel/projects/ralph-hero/knowledge.db`
+
+> **Tip:** For consistent DB location, add to `.claude/settings.local.json`:
+> ```json
+> {
+>   "env": {
+>     "RALPH_KNOWLEDGE_DB": "/home/chad_a_dubiel/projects/ralph-hero/knowledge.db"
+>   }
+> }
+> ```
+
+## Step 3: Install and run reindex
+
+**[SKIPPED - test run]** Would run the following commands:
+
+```bash
+cd /tmp && npm install --no-save ralph-hero-knowledge-index@latest 2>&1 | tail -3
+node /tmp/node_modules/ralph-hero-knowledge-index/dist/reindex.js /home/chad_a_dubiel/projects/ralph-hero/thoughts/ /home/chad_a_dubiel/projects/ralph-hero/knowledge.db
+```
+
+This would:
+- Scan all 454 `.md` files recursively (skipping dot-directories)
+- Parse frontmatter (title, date, type, status, tags)
+- Extract `## Prior Work` relationships (builds_on, tensions, superseded_by)
+- Build FTS5 full-text search index
+- Generate 384-dim semantic embeddings via all-MiniLM-L6-v2
+- Store everything in the SQLite database
+
+Note: An existing `knowledge.db` (6.1 MB) was found at the project root, so this would be a reindex/rebuild.
+
+## Step 4: Verify
+
+Since the database already exists, ran a verification search:
+
+```
+knowledge_search(query="recent research", limit=3)
+```
+
+**Results (3 documents returned):**
+
+| # | Document | Type | Date | Score |
+|---|----------|------|------|-------|
+| 1 | "Hello" Session Briefing Command | idea | 2026-03-01 | 0.016 |
+| 2 | Idea Hunt Synthesis: What's Actually Interesting Out There | idea | -- | 0.016 |
+| 3 | Research: `/hello` Session Briefing Command (GH-480) | research | 2026-03-03 | 0.016 |
+
+Search is working. Both `knowledge_search` and `knowledge_traverse` tools are connected and operational.
+
+## Step 5: Summary
+
+```
+Knowledge Index Ready
+=====================
+Documents indexed: 454
+Database: /home/chad_a_dubiel/projects/ralph-hero/knowledge.db
+Thoughts directory: /home/chad_a_dubiel/projects/ralph-hero/thoughts/
+
+Tools available:
+  - knowledge_search: Keyword + semantic search across documents
+  - knowledge_traverse: Walk relationship edges between documents
+
+To reindex after adding new documents:
+  /ralph-knowledge:setup /home/chad_a_dubiel/projects/ralph-hero/thoughts/
+```
+
+## Prerequisites Check Summary
+
+| Check | Status |
+|-------|--------|
+| `knowledge_search` tool available | PASS |
+| `knowledge_traverse` tool available | PASS |
+| Thoughts directory found | PASS (454 files) |
+| Database exists | PASS (6.1 MB at project root) |
+| `RALPH_KNOWLEDGE_DB` env var set | NOT SET (using default) |
+| Verification search returns results | PASS (3 results) |

package/skills/setup-workspace/iteration-1/eval-first-time-setup/with_skill/timing.json

@@ -0,0 +1,5 @@
+{
+  "total_tokens": 22885,
+  "duration_ms": 61878,
+  "total_duration_seconds": 61.9
+}

package/skills/setup-workspace/iteration-1/eval-first-time-setup/without_skill/outputs/output.md

@@ -0,0 +1,86 @@
+# Baseline Eval: Set Up ralph-knowledge (Without Skill Guidance)
+
+## Task
+
+"Set up ralph-knowledge" — first-time setup of the knowledge index for the `thoughts/` directory (454 markdown files).
+
+## What I Found
+
+### Current State
+
+The `ralph-knowledge` plugin does **not exist yet** as implemented code. Here is what exists:
+
+1. **Design doc**: `docs/plans/2026-03-08-knowledge-graph-design.md` — describes the full architecture (SQLite + FTS5 + sqlite-vec + embeddings), document format (wikilinks, Prior Work sections), MCP tools (`knowledge_search`, `knowledge_traverse`), and the indexer.
+
+2. **Implementation plan**: `docs/plans/2026-03-08-knowledge-graph-impl.md` — a 10-task plan (Part A: 3 tasks for innate document protocol, Part B: 7 tasks for the optional knowledge-index plugin). Contains complete source code for every file.
+
+3. **Empty plugin directory**: `plugin/ralph-knowledge/skills/setup-workspace/iteration-1/` exists with empty `outputs/` directories for evaluation scaffolding, but no actual plugin code (no `package.json`, no `src/`, no `.mcp.json`, no MCP server).
+
+4. **No `knowledge-index` directory**: `plugin/ralph-hero/knowledge-index/` does not exist. The impl plan specifies this as the location for the MCP server.
+
+5. **Existing `.mcp.json`**: `plugin/ralph-hero/.mcp.json` only registers `ralph-github` (the main MCP server via `npx ralph-hero-mcp-server@2.5.4`). There is no `ralph-knowledge` entry.
+
+6. **454 markdown files** exist in `thoughts/` across subdirectories: `ideas/`, `shared/ideas/`, `shared/plans/`, `shared/reports/`, `shared/research/`, `shared/reviews/`.
+
+### What "Set Up ralph-knowledge" Requires
+
+Based on the design and implementation plan, setting up ralph-knowledge requires building the entire knowledge-index MCP server from scratch:
+
+#### Part B of the Implementation Plan (7 tasks):
+
+| Task | Description | Status |
+|------|-------------|--------|
+| B1 | Project scaffold (package.json, tsconfig.json, npm install) | Not started |
+| B2 | Markdown parser (frontmatter, wikilinks, relationships) | Not started |
+| B3 | SQLite schema and document storage (KnowledgeDB class) | Not started |
+| B4 | FTS5 full-text search (FtsSearch class) | Not started |
+| B5 | Relationship traversal (Traverser class with recursive CTEs) | Not started |
+| B6 | Embedding generation and vector search (sqlite-vec + HuggingFace) | Not started |
+| B7 | Hybrid search (RRF over FTS5 + vectors) | Not started |
+| B8 | MCP server with both tools (knowledge_search, knowledge_traverse) | Not started |
+| B9 | Reindex script (scan thoughts/, parse, embed, build index) | Not started |
+| B10 | Wire into .mcp.json | Not started |
+
+#### Dependencies Required:
+- `better-sqlite3` ^12.6.0 (SQLite driver)
+- `sqlite-vec` ^0.1.7-alpha.10 (vector similarity)
+- `@huggingface/transformers` ^3.0.0 (~80MB model download on first run)
+- `@modelcontextprotocol/sdk` ^1.26.0
+- `yaml` ^2.7.0
+- `zod` ^3.25.0
+- `vitest` ^4.0.0 (dev)
+- `typescript` ^5.7.0 (dev)
+
+#### After Building, the Setup Steps Would Be:
+
+1. `cd plugin/ralph-hero/knowledge-index && npm install` — install dependencies
+2. `npm run build` — compile TypeScript
+3. `node dist/reindex.js ../../thoughts knowledge.db` — index all 454 markdown files (first run downloads ~80MB embedding model to `~/.cache/huggingface/hub/`)
+4. Add `ralph-knowledge` entry to `plugin/ralph-hero/.mcp.json`
+5. Restart Claude Code to pick up the new MCP server
+
+## What I Did
+
+1. **Explored** the `plugin/ralph-knowledge/` directory — found only empty eval scaffolding.
+2. **Read** both design and implementation plan documents in full.
+3. **Checked** `plugin/ralph-hero/knowledge-index/` — does not exist.
+4. **Checked** `.mcp.json` — only `ralph-github` is registered.
+5. **Verified** the `thoughts/` directory has 454 markdown files ready to index.
+6. **Did NOT attempt to build the plugin** because:
+   - The implementation plan is a 10-task, multi-file project (~1000+ lines of TypeScript)
+   - It requires native C++ dependencies (`better-sqlite3`, `sqlite-vec`) and a large ML model download
+   - Building it without explicit instruction to implement the full plan would be overstepping the "set up" request
+
+## Blockers
+
+**The knowledge-index MCP server has not been implemented yet.** There is no code to set up, configure, or run. The `knowledge_search` and `knowledge_traverse` MCP tools listed in the available deferred tools appear to exist in the tool registry, but the underlying server code at `plugin/ralph-hero/knowledge-index/` has not been created.
+
+To proceed, someone needs to execute the implementation plan at `docs/plans/2026-03-08-knowledge-graph-impl.md` (Tasks B1-B10), which would create all the source files, build the MCP server, and run the initial index.
+
+## Outcome
+
+**Could not complete setup.** The ralph-knowledge plugin is in design/planning phase only — no implementation exists to set up. The design docs are comprehensive and contain complete source code for every file, but the code has not been written to disk yet.
+
+## Confidence
+
+High confidence that I correctly identified the situation. The task cannot be completed without first implementing the knowledge-index MCP server per the implementation plan.

package/skills/setup-workspace/iteration-1/eval-first-time-setup/without_skill/timing.json

@@ -0,0 +1,5 @@
+{
+  "total_tokens": 53012,
+  "duration_ms": 99582,
+  "total_duration_seconds": 99.6
+}

package/skills/setup-workspace/iteration-1/eval-reindex-explicit-path/with_skill/outputs/output.md

@@ -0,0 +1,75 @@
+# Ralph Knowledge Setup
+
+## Step 1: Locate Thoughts Directory
+
+Explicit path provided as argument: `/home/chad_a_dubiel/projects/ralph-hero/thoughts`
+
+Found thoughts directory: `/home/chad_a_dubiel/projects/ralph-hero/thoughts`
+Contains **454** markdown files.
+
+Proceed with indexing? **yes**
+
+## Step 2: Determine DB Path
+
+`RALPH_KNOWLEDGE_DB` is not set in the environment.
+
+Existing database found at: `/home/chad_a_dubiel/projects/ralph-hero/knowledge.db` (5.8 MB)
+
+Using default path: `knowledge.db` (resolves relative to MCP server working directory).
+
+> Tip: For consistent DB location, add to `.claude/settings.local.json`:
+> ```json
+> {
+>   "env": {
+>     "RALPH_KNOWLEDGE_DB": "/home/chad_a_dubiel/projects/ralph-hero/knowledge.db"
+>   }
+> }
+> ```
+
+## Step 3: Reindex
+
+**[SKIPPED - test run]** Would run the following commands:
+
+```bash
+cd /tmp && npm install --no-save ralph-hero-knowledge-index@latest 2>&1 | tail -3
+node /tmp/node_modules/ralph-hero-knowledge-index/dist/reindex.js /home/chad_a_dubiel/projects/ralph-hero/thoughts /home/chad_a_dubiel/projects/ralph-hero/knowledge.db
+```
+
+This would:
+- Scan 454 `.md` files recursively (skipping dot-directories)
+- Parse frontmatter (title, date, type, status, tags)
+- Extract `## Prior Work` relationships (builds_on, tensions, superseded_by)
+- Build FTS5 full-text search index
+- Generate 384-dim semantic embeddings via all-MiniLM-L6-v2
+- Store everything in the SQLite database
+
+## Step 4: Verify
+
+Ran test search: `knowledge_search(query="recent research", limit=3)`
+
+Results returned successfully:
+
+| # | Document | Type | Date | Score |
+|---|----------|------|------|-------|
+| 1 | "Hello" Session Briefing Command | idea | 2026-03-01 | 0.016 |
+| 2 | Idea Hunt Synthesis: What's Actually Interesting Out There | idea | -- | 0.016 |
+| 3 | Research: `/hello` Session Briefing Command (GH-480) | research | 2026-03-03 | 0.016 |
+
+Knowledge search is working. The existing database is valid and returning results.
+
+## Step 5: Summary
+
+```
+Knowledge Index Ready
+=====================
+Documents indexed: 454 markdown files in thoughts directory
+Database: /home/chad_a_dubiel/projects/ralph-hero/knowledge.db
+Thoughts directory: /home/chad_a_dubiel/projects/ralph-hero/thoughts
+
+Tools available:
+  - knowledge_search: Keyword + semantic search across documents
+  - knowledge_traverse: Walk relationship edges between documents
+
+To reindex after adding new documents:
+  /ralph-knowledge:setup /home/chad_a_dubiel/projects/ralph-hero/thoughts
+```

package/skills/setup-workspace/iteration-1/eval-reindex-explicit-path/with_skill/timing.json

@@ -0,0 +1,5 @@
+{
+  "total_tokens": 22801,
+  "duration_ms": 61340,
+  "total_duration_seconds": 61.3
+}

package/skills/setup-workspace/iteration-1/eval-reindex-explicit-path/without_skill/outputs/output.md

@@ -0,0 +1,71 @@
+# Reindex Knowledge Base - Without Skill
+
+## Task
+
+Reindex the knowledge base from `/home/chad_a_dubiel/projects/ralph-hero/thoughts`.
+
+## Approach
+
+Without any skill guidance, I investigated the knowledge plugin structure through the following steps:
+
+1. **Explored the plugin directory** at `plugin/ralph-knowledge/` -- found it contained only a `skills/` directory with eval scaffolding (no local source code).
+
+2. **Identified the npm package** `ralph-hero-knowledge-index` referenced in the `.mcp.json` at `plugin/ralph-knowledge/.mcp.json`. The MCP server config showed:
+   - Command: `npx -y ralph-hero-knowledge-index@0.1.4`
+   - Environment: `RALPH_KNOWLEDGE_DB` defaulting to `knowledge.db`
+
+3. **Inspected the npm package** using `npm view ralph-hero-knowledge-index scripts` which revealed:
+   - `reindex`: `node dist/reindex.js` -- the script needed for reindexing
+   - `start`: `node dist/index.js` -- the MCP server entrypoint
+   - The `bin` entry points to `dist/index.js` (MCP server), not the reindex script
+
+4. **Read the `reindex.js` source** from the npx cache to understand its interface:
+   - `argv[2]`: thoughts directory path (defaults to `../../thoughts`)
+   - `argv[3]`: database file path (defaults to `knowledge.db`)
+   - Walks the directory recursively for `.md` files
+   - Parses each document (extracting title, date, type, status, tags, relationships)
+   - Builds FTS (full-text search) index
+   - Generates vector embeddings using `@huggingface/transformers`
+   - Stores everything in a SQLite database with `sqlite-vec` extension
+
+5. **Found existing `knowledge.db`** at the project root (`/home/chad_a_dubiel/projects/ralph-hero/knowledge.db`).
+
+6. **Ran the reindex** by invoking `reindex.js` directly via node from the npx cache:
+   ```
+   node <npx-cache>/ralph-hero-knowledge-index/dist/reindex.js \
+     /home/chad_a_dubiel/projects/ralph-hero/thoughts \
+     /home/chad_a_dubiel/projects/ralph-hero/knowledge.db
+   ```
+
+## Challenges
+
+- **The npm `bin` entrypoint is the MCP server**, not the reindex script. Running `npx ralph-hero-knowledge-index` starts the MCP server, not the reindexer.
+- **No `npm run reindex` available via npx** -- the `reindex` script is defined in `package.json` but npx only exposes the `bin` entry, not npm scripts.
+- **Had to locate `reindex.js` in the npx cache** and invoke it directly with `node`. This is fragile because the npx cache path is a hash that can change.
+- **No documentation about how to run reindex** was available in the plugin directory or CLAUDE.md. Had to reverse-engineer the process from the npm package metadata and source code.
+
+## Result
+
+```
+Indexing /home/chad_a_dubiel/projects/ralph-hero/thoughts -> /home/chad_a_dubiel/projects/ralph-hero/knowledge.db
+Found 454 markdown files
+dtype not specified for "model". Using the default dtype (fp32) for this device (cpu).
+  50/454 indexed
+  100/454 indexed
+  150/454 indexed
+  200/454 indexed
+  250/454 indexed
+  300/454 indexed
+  350/454 indexed
+  400/454 indexed
+  450/454 indexed
+Done. 454 documents indexed.
+```
+
+Successfully indexed 454 markdown documents into `knowledge.db` with full-text search and vector embeddings.
+
+## Time & Effort Assessment
+
+- Required ~8 tool calls to investigate and understand the reindex process before being able to run it
+- Key friction points: no documented reindex command, bin entrypoint mismatch, npx cache dependency
+- A skill could streamline this to a single guided command

package/skills/setup-workspace/iteration-1/eval-reindex-explicit-path/without_skill/timing.json

@@ -0,0 +1,5 @@
+{
+  "total_tokens": 29535,
+  "duration_ms": 118665,
+  "total_duration_seconds": 118.7
+}

package/skills/setup-workspace/iteration-1/eval-troubleshooting/with_skill/outputs/output.md

@@ -0,0 +1,96 @@
+# Troubleshooting: knowledge_search Returns Empty Results
+
+## Diagnosis
+
+### Step 1: Verified MCP Server Connectivity
+
+The `knowledge_search` and `knowledge_traverse` tools are both available and connected. No MCP server connectivity issue.
+
+### Step 2: Tested knowledge_search
+
+Ran a test query:
+
+```
+knowledge_search(query="recent research", limit=3)
+```
+
+**Result: Search returned 3 results successfully.** The tool is working.
+
+Results returned:
+1. `2026-03-01-hello-session-briefing` (thoughts/shared/ideas/) - score: 0.016
+2. `2026-02-25-idea-hunt-synthesis` (thoughts/shared/ideas/) - score: 0.016
+3. `2026-03-03-GH-0480-hello-session-briefing` (thoughts/shared/research/) - score: 0.016
+
+### Step 3: Checked the Database
+
+- **DB exists**: `/home/chad_a_dubiel/projects/ralph-hero/knowledge.db` (5.8 MB, last modified Mar 9 15:19)
+- **`RALPH_KNOWLEDGE_DB` env var**: Not explicitly set -- the MCP server is using its default path resolution, which found the DB at the project root.
+
+### Step 4: Checked the Thoughts Directory
+
+- **Location**: `/home/chad_a_dubiel/projects/ralph-hero/thoughts/`
+- **Contents**: 454 markdown files indexed
+
+## Findings
+
+The `knowledge_search` tool is **currently working**. If you were previously getting empty results, here are the most likely causes and how to prevent recurrence:
+
+### Common Causes of Empty Results
+
+1. **DB path mismatch**: The most common cause. If `RALPH_KNOWLEDGE_DB` is not set, the MCP server resolves `knowledge.db` relative to its own working directory. If the server's working directory changes (e.g., running from a worktree), it may look for the DB in a different location than where reindex wrote it.
+
+   **Fix**: Set an absolute path in `.claude/settings.local.json`:
+   ```json
+   {
+     "env": {
+       "RALPH_KNOWLEDGE_DB": "/home/chad_a_dubiel/projects/ralph-hero/knowledge.db"
+     }
+   }
+   ```
+
+2. **Stale or empty DB**: If the DB file exists but was never populated (e.g., reindex failed partway through), searches return empty.
+
+   **Fix**: Re-run the reindex:
+   ```bash
+   cd /tmp && npm install --no-save ralph-hero-knowledge-index@latest 2>&1 | tail -3
+   node /tmp/node_modules/ralph-hero-knowledge-index/dist/reindex.js /home/chad_a_dubiel/projects/ralph-hero/thoughts /home/chad_a_dubiel/projects/ralph-hero/knowledge.db
+   ```
+
+3. **MCP server reading a different DB copy**: If there are multiple `knowledge.db` files (e.g., one in the project root, one in a worktree), the server may read a different copy than the one you indexed into.
+
+   **Fix**: Search for duplicate DB files and set the explicit absolute path as shown above.
+
+4. **Query too specific**: If searching for a very narrow term that doesn't appear in any indexed document, results will be empty. Try broader queries like "research" or "plan".
+
+## Recommendation
+
+Since `RALPH_KNOWLEDGE_DB` is not currently set explicitly, I recommend adding it to prevent future path-resolution issues:
+
+Add to `.claude/settings.local.json`:
+```json
+{
+  "env": {
+    "RALPH_KNOWLEDGE_DB": "/home/chad_a_dubiel/projects/ralph-hero/knowledge.db"
+  }
+}
+```
+
+This ensures the MCP server always finds the DB regardless of working directory.
+
+## Current Status
+
+```
+Knowledge Index Status
+======================
+Documents indexed: 454
+Database: /home/chad_a_dubiel/projects/ralph-hero/knowledge.db (5.8 MB)
+Thoughts directory: /home/chad_a_dubiel/projects/ralph-hero/thoughts/
+MCP server: Connected and responding
+
+Tools available:
+  - knowledge_search: Working (verified with test query)
+  - knowledge_traverse: Connected (available)
+
+To reindex after adding new documents:
+  /ralph-knowledge:setup /home/chad_a_dubiel/projects/ralph-hero/thoughts
+```

package/skills/setup-workspace/iteration-1/eval-troubleshooting/with_skill/timing.json

@@ -0,0 +1,5 @@
+{
+  "total_tokens": 22847,
+  "duration_ms": 49408,
+  "total_duration_seconds": 49.4
+}

package/skills/setup-workspace/iteration-1/eval-troubleshooting/without_skill/outputs/output.md

@@ -0,0 +1,133 @@
+# Troubleshooting: knowledge_search Returns Empty Results
+
+## Task
+
+User reported that `knowledge_search` returns empty results. Diagnose and fix the issue without any skill guidance.
+
+## Diagnostic Process
+
+### Step 1: Test the tool directly
+
+Called `knowledge_search` with query `"knowledge graph"`. Result: **10 results returned successfully.**
+
+The tool is technically working in the current session. This suggests the "empty results" problem is environment-dependent -- it depends on which database file the MCP server connects to.
+
+### Step 2: Locate the database files
+
+Found two `knowledge.db` files:
+
+| File | Size | Documents | FTS Index | Vector Index |
+|------|------|-----------|-----------|-------------|
+| `/home/chad_a_dubiel/projects/ralph-hero/knowledge.db` | 6 MB | 394 | Yes (394 entries) | Yes (394 entries) |
+| `/home/chad_a_dubiel/projects/ralph-hero/.claude/worktrees/knowledge-graph/knowledge.db` | 36 KB | **0** | **Missing** | **Missing** |
+
+The worktree database is completely empty -- it has the schema tables (`documents`, `tags`, `relationships`) created by `KnowledgeDB.createSchema()` but zero rows and no FTS5 or sqlite-vec virtual tables.
+
+### Step 3: Understand how the DB path resolves
+
+The `.mcp.json` in the ralph-knowledge plugin configures:
+
+```json
+{
+  "env": {
+    "RALPH_KNOWLEDGE_DB": "${RALPH_KNOWLEDGE_DB:-knowledge.db}"
+  }
+}
+```
+
+And `index.ts` reads:
+
+```typescript
+const dbPath = process.env.RALPH_KNOWLEDGE_DB ?? "knowledge.db";
+```
+
+Since `RALPH_KNOWLEDGE_DB` is **not set** in either `.claude/settings.local.json` (main repo or worktree), the server uses the default `knowledge.db` -- a **relative path** that resolves from the MCP server's working directory.
+
+- When running from the **main repo** (`/home/chad_a_dubiel/projects/ralph-hero/`), it finds the populated 6MB database.
+- When running from a **worktree** (e.g., `.claude/worktrees/knowledge-graph/`), it finds (or creates) an empty database at that location.
+
+### Step 4: Check if indexing has been run
+
+The worktree has 436 markdown files in `thoughts/`, but they have never been indexed. The `reindex.ts` script (`npm run reindex`) must be run explicitly to populate the database. It is **not** run automatically when the MCP server starts.
+
+### Step 5: Check plugin enablement
+
+- **Main repo** `.claude/settings.local.json`: Has `"ralph-knowledge@ralph-hero": true` in `enabledPlugins`.
+- **Worktree** `.claude/settings.local.json`: Does **not** have `ralph-knowledge@ralph-hero` in `enabledPlugins`.
+
+## Root Cause
+
+**The knowledge database has never been indexed.** The `reindex` command (which scans `thoughts/` markdown files, parses frontmatter, builds FTS5 full-text search index, and generates semantic embeddings) must be run before `knowledge_search` can return results.
+
+The secondary cause is that `RALPH_KNOWLEDGE_DB` is a relative path (`knowledge.db`), which means different working directories create/read different database files. The main repo happens to have a populated one, but worktrees and fresh setups will not.
+
+## Fix
+
+### Immediate Fix: Run the reindex command
+
+```bash
+cd /tmp && npm install --no-save ralph-hero-knowledge-index@latest 2>&1 | tail -3
+node /tmp/node_modules/ralph-hero-knowledge-index/dist/reindex.js /path/to/thoughts knowledge.db
+```
+
+Or from the plugin source directory:
+
+```bash
+cd plugin/ralph-knowledge
+npm run build
+node dist/reindex.js ../../thoughts /home/chad_a_dubiel/projects/ralph-hero/knowledge.db
+```
+
+### Permanent Fix: Set an absolute DB path
+
+Add `RALPH_KNOWLEDGE_DB` to `.claude/settings.local.json` with an absolute path so all worktrees and sessions use the same database:
+
+```json
+{
+  "env": {
+    "RALPH_KNOWLEDGE_DB": "/home/chad_a_dubiel/projects/ralph-hero/knowledge.db"
+  }
+}
+```
+
+This ensures the MCP server always connects to the populated database regardless of working directory.
+
+### Optional: Enable the plugin in the worktree
+
+If using the worktree, add to `.claude/worktrees/knowledge-graph/.claude/settings.local.json`:
+
+```json
+{
+  "enabledPlugins": {
+    "ralph-knowledge@ralph-hero": true
+  }
+}
+```
+
+## Summary of Findings
+
+| Check | Result |
+|-------|--------|
+| MCP server running | Yes |
+| Tool accessible | Yes |
+| Database exists | Yes (but empty in worktree) |
+| Documents indexed | No (0 documents in worktree DB) |
+| FTS index built | No (table missing in worktree DB) |
+| Vector index built | No (table missing in worktree DB) |
+| `RALPH_KNOWLEDGE_DB` env var set | No (defaults to relative `knowledge.db`) |
+| `thoughts/` directory exists | Yes (436 markdown files) |
+| `reindex` has been run | No |
+
+## What I Could Not Do Without Skill Guidance
+
+1. **I did not know the exact reindex invocation** without reading the source code. The skill (`skills/setup/SKILL.md`) documents the exact `npm install` + `node reindex.js` command, but I had to discover this by reading `reindex.ts` and `package.json` manually.
+
+2. **I was uncertain about the recommended DB path strategy.** The skill's step 2 explicitly recommends setting an absolute path in `settings.local.json`. Without the skill, I had to infer this from the `.mcp.json` fallback pattern and the observed relative-path problem.
+
+3. **I did not run the actual fix** (reindexing) because it would take significant time (downloading the embedding model on first run, processing 400+ documents) and I wanted to confirm the diagnosis first. The skill would have guided me through the interactive confirmation flow.
+
+4. **The verification step** (running `knowledge_search` after reindex) is documented in the skill but I arrived at it independently by testing the tool directly.
+
+## Conclusion
+
+The root cause is straightforward: the knowledge database needs to be populated by running the `reindex` command against the `thoughts/` directory. The fix is a two-step process: (1) run reindex to populate the database, and (2) optionally set `RALPH_KNOWLEDGE_DB` to an absolute path to prevent the relative-path ambiguity across different working directories and worktrees.

package/skills/setup-workspace/iteration-1/eval-troubleshooting/without_skill/timing.json

@@ -0,0 +1,5 @@
+{
+  "total_tokens": 48010,
+  "duration_ms": 151254,
+  "total_duration_seconds": 151.3
+}

package/src/__tests__/parser.test.ts

@@ -97,4 +97,87 @@ describe("parseDocument", () => {
     expect(doc.content).toContain("current cache has no TTL");
     expect(doc.content).not.toContain("---");
   });
+
+  describe("githubIssue fallback chain", () => {
+    function makeDoc(frontmatter: string, body = "# Test\n\nContent."): string {
+      return `---\n${frontmatter}\n---\n\n${body}`;
+    }
+
+    it("falls back to github_issues[0] when github_issue is absent", () => {
+      const raw = makeDoc("github_issues: [42, 43, 44]");
+      const doc = parseDocument("test", "test.md", raw);
+      expect(doc.githubIssue).toBe(42);
+    });
+
+    it("falls back to primary_issue when both github_issue and github_issues are absent", () => {
+      const raw = makeDoc("primary_issue: 42");
+      const doc = parseDocument("test", "test.md", raw);
+      expect(doc.githubIssue).toBe(42);
+    });
+
+    it("prefers github_issue over github_issues and primary_issue", () => {
+      const raw = makeDoc("github_issue: 10\ngithub_issues: [20, 30]\nprimary_issue: 40");
+      const doc = parseDocument("test", "test.md", raw);
+      expect(doc.githubIssue).toBe(10);
+    });
+
+    it("prefers github_issues[0] over primary_issue when github_issue is absent", () => {
+      const raw = makeDoc("github_issues: [20, 30]\nprimary_issue: 40");
+      const doc = parseDocument("test", "test.md", raw);
+      expect(doc.githubIssue).toBe(20);
+    });
+
+    it("returns null for empty github_issues array with no other fallbacks", () => {
+      const raw = makeDoc("github_issues: []");
+      const doc = parseDocument("test", "test.md", raw);
+      expect(doc.githubIssue).toBeNull();
+    });
+
+    it("returns null when primary_issue is null", () => {
+      const raw = makeDoc("primary_issue: null");
+      const doc = parseDocument("test", "test.md", raw);
+      expect(doc.githubIssue).toBeNull();
+    });
+
+    it("returns null when no issue fields are present", () => {
+      const raw = makeDoc("status: draft\ntype: plan");
+      const doc = parseDocument("test", "test.md", raw);
+      expect(doc.githubIssue).toBeNull();
+    });
+
+    it("returns null when github_issues contains non-number first element", () => {
+      const raw = makeDoc('github_issues: ["not-a-number"]');
+      const doc = parseDocument("test", "test.md", raw);
+      expect(doc.githubIssue).toBeNull();
+    });
+
+    it("handles typical group plan frontmatter with all fields", () => {
+      const raw = makeDoc([
+        "date: 2026-03-09",
+        "status: draft",
+        "type: plan",
+        "github_issue: 550",
+        "github_issues: [550, 551, 552]",
+        "primary_issue: 550",
+        "tags: [knowledge-graph, metadata]",
+      ].join("\n"));
+      const doc = parseDocument("test-plan", "thoughts/shared/plans/test-plan.md", raw);
+      expect(doc.githubIssue).toBe(550);
+      expect(doc.type).toBe("plan");
+      expect(doc.tags).toEqual(["knowledge-graph", "metadata"]);
+    });
+
+    it("handles plan with only github_issues array (no singular)", () => {
+      const raw = makeDoc([
+        "date: 2026-03-09",
+        "status: draft",
+        "type: plan",
+        "github_issues: [550, 551, 552]",
+        "primary_issue: 550",
+        "tags: [knowledge-graph]",
+      ].join("\n"));
+      const doc = parseDocument("test-plan", "thoughts/shared/plans/test-plan.md", raw);
+      expect(doc.githubIssue).toBe(550);
+    });
+  });
 });

package/src/__tests__/reindex.test.ts

@@ -0,0 +1,35 @@
+import { describe, it, expect } from "vitest";
+import { mkdtempSync, writeFileSync, mkdirSync } from "node:fs";
+import { join } from "node:path";
+import { tmpdir } from "node:os";
+import { findMarkdownFiles } from "../reindex.js";
+
+describe("findMarkdownFiles", () => {
+  it("finds .md files recursively", () => {
+    const dir = mkdtempSync(join(tmpdir(), "knowledge-test-"));
+    writeFileSync(join(dir, "a.md"), "# A");
+    mkdirSync(join(dir, "sub"));
+    writeFileSync(join(dir, "sub", "b.md"), "# B");
+    writeFileSync(join(dir, "c.txt"), "not markdown");
+
+    const files = findMarkdownFiles(dir);
+    expect(files).toHaveLength(2);
+    expect(files.every(f => f.endsWith(".md"))).toBe(true);
+  });
+
+  it("skips dot-directories", () => {
+    const dir = mkdtempSync(join(tmpdir(), "knowledge-test-"));
+    mkdirSync(join(dir, ".hidden"));
+    writeFileSync(join(dir, ".hidden", "secret.md"), "# Hidden");
+    writeFileSync(join(dir, "visible.md"), "# Visible");
+
+    const files = findMarkdownFiles(dir);
+    expect(files).toHaveLength(1);
+  });
+
+  it("returns empty for empty directory", () => {
+    const dir = mkdtempSync(join(tmpdir(), "knowledge-test-"));
+    const files = findMarkdownFiles(dir);
+    expect(files).toHaveLength(0);
+  });
+});

package/src/parser.ts

@@ -57,7 +57,13 @@ export function parseDocument(id: string, path: string, raw: string): ParsedDocu
     date: frontmatter.date ? String(frontmatter.date) : null,
     type: frontmatter.type ?? null,
     status: frontmatter.status ?? null,
-    githubIssue: typeof frontmatter.github_issue === "number" ? frontmatter.github_issue : null,
+    githubIssue: typeof frontmatter.github_issue === "number"
+      ? frontmatter.github_issue
+      : Array.isArray(frontmatter.github_issues) && typeof frontmatter.github_issues[0] === "number"
+        ? frontmatter.github_issues[0]
+        : typeof frontmatter.primary_issue === "number"
+          ? frontmatter.primary_issue
+          : null,
     tags, relationships, content: body,
   };
 }

package/src/reindex.ts

@@ -1,5 +1,5 @@
 import { readFileSync, readdirSync } from "node:fs";
-import { join, relative, basename } from "node:path";
+import { join, relative, resolve, basename } from "node:path";
 import { homedir } from "node:os";
 import { KnowledgeDB } from "./db.js";
 import { FtsSearch } from "./search.js";
@@ -7,7 +7,7 @@ import { VectorSearch } from "./vector-search.js";
 import { embed, prepareTextForEmbedding } from "./embedder.js";
 import { parseDocument } from "./parser.js";
 
-function findMarkdownFiles(dir: string): string[] {
+export function findMarkdownFiles(dir: string): string[] {
   const results: string[] = [];
   function walk(d: string) {
     for (const entry of readdirSync(d, { withFileTypes: true })) {
@@ -23,8 +23,8 @@ function findMarkdownFiles(dir: string): string[] {
   return results;
 }
 
-async function reindex(thoughtsDir: string, dbPath: string): Promise<void> {
-  console.log(`Indexing ${thoughtsDir} -> ${dbPath}`);
+export async function reindex(dirs: string[], dbPath: string): Promise<void> {
+  console.log(`Indexing ${dirs.join(", ")} -> ${dbPath}`);
 
   const db = new KnowledgeDB(dbPath);
   const fts = new FtsSearch(db);
@@ -35,13 +35,22 @@ async function reindex(thoughtsDir: string, dbPath: string): Promise<void> {
   vec.dropIndex();
   vec.createIndex();
 
-  const files = findMarkdownFiles(thoughtsDir);
-  console.log(`Found ${files.length} markdown files`);
+  const files: string[] = [];
+  for (const dir of dirs) {
+    const found = findMarkdownFiles(dir);
+    console.log(`  ${dir}: ${found.length} files`);
+    files.push(...found);
+  }
+  console.log(`Found ${files.length} total markdown files`);
 
   let indexed = 0;
   for (const filePath of files) {
     const raw = readFileSync(filePath, "utf-8");
-    const relPath = relative(join(thoughtsDir, ".."), filePath);
+    const absPath = resolve(filePath);
+    const sourceDir = dirs.find(d => absPath.startsWith(resolve(d)));
+    const relPath = sourceDir
+      ? relative(resolve(sourceDir, ".."), absPath)
+      : filePath;
     const id = basename(filePath, ".md");
 
     const parsed = parseDocument(id, relPath, raw);
@@ -87,6 +96,28 @@ async function reindex(thoughtsDir: string, dbPath: string): Promise<void> {
 
 const DEFAULT_DB_PATH = join(homedir(), ".ralph-hero", "knowledge.db");
 
-const thoughtsDir = process.argv[2] ?? "../../thoughts";
-const dbPath = process.argv[3] ?? DEFAULT_DB_PATH;
-reindex(thoughtsDir, dbPath).catch(console.error);
+export function resolveDirs(): { dirs: string[]; dbPath: string } {
+  const cliArgs = process.argv.slice(2);
+  const cliDb = cliArgs.find(a => a.endsWith(".db"));
+  const cliDirs = cliArgs.filter(a => !a.endsWith(".db"));
+
+  if (cliDirs.length > 0) {
+    return { dirs: cliDirs, dbPath: cliDb ?? DEFAULT_DB_PATH };
+  }
+
+  const envDirs = process.env.RALPH_KNOWLEDGE_DIRS;
+  if (envDirs) {
+    return {
+      dirs: envDirs.split(",").map(d => d.trim()).filter(Boolean),
+      dbPath: cliDb ?? process.env.RALPH_KNOWLEDGE_DB ?? DEFAULT_DB_PATH,
+    };
+  }
+
+  return { dirs: ["../../thoughts"], dbPath: cliDb ?? DEFAULT_DB_PATH };
+}
+
+const isMain = process.argv[1]?.endsWith("reindex.js");
+if (isMain) {
+  const { dirs, dbPath } = resolveDirs();
+  reindex(dirs, dbPath).catch(console.error);
+}