@autonav/core 1.3.0 → 1.3.2

package/dist/migrations/index.d.ts

@@ -0,0 +1,38 @@
+/**
+ * Migration system
+ *
+ * Manages versioned migrations that bring navigators up to spec with
+ * latest best practices.
+ */
+import type { Migration, MigrationCheck, MigrationResult } from "./types.js";
+/**
+ * Get the current version of a navigator
+ */
+export declare function getNavigatorVersion(navPath: string): string | null;
+/**
+ * Check which migrations are needed for a navigator
+ */
+export declare function checkMigrations(navPath: string): Promise<Array<{
+    migration: Migration;
+    check: MigrationCheck;
+}>>;
+/**
+ * Apply a specific migration to a navigator
+ */
+export declare function applyMigration(navPath: string, migration: Migration, confirm: (action: string, details: string) => Promise<boolean>): Promise<MigrationResult>;
+/**
+ * Apply all needed migrations to a navigator
+ */
+export declare function applyAllMigrations(navPath: string, confirm: (action: string, details: string) => Promise<boolean>): Promise<{
+    results: Array<{
+        migration: Migration;
+        result: MigrationResult;
+    }>;
+    success: boolean;
+}>;
+/**
+ * Get all available migrations
+ */
+export declare function getAllMigrations(): Migration[];
+export type { Migration, MigrationCheck, MigrationResult, ConfirmFn } from "./types.js";
+//# sourceMappingURL=index.d.ts.map

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

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package/dist/migrations/index.js

@@ -0,0 +1,74 @@
+/**
+ * Migration system
+ *
+ * Manages versioned migrations that bring navigators up to spec with
+ * latest best practices.
+ */
+import * as fs from "node:fs";
+import * as path from "node:path";
+import { migration as v1_3_1_submitAnswer } from "./versions/v1.3.1-submit-answer.js";
+/**
+ * All available migrations in order
+ */
+const MIGRATIONS = [
+    v1_3_1_submitAnswer,
+];
+/**
+ * Get the current version of a navigator
+ */
+export function getNavigatorVersion(navPath) {
+    const configPath = path.join(navPath, "config.json");
+    if (!fs.existsSync(configPath)) {
+        return null;
+    }
+    try {
+        const config = JSON.parse(fs.readFileSync(configPath, "utf-8"));
+        return config.version || null;
+    }
+    catch {
+        return null;
+    }
+}
+/**
+ * Check which migrations are needed for a navigator
+ */
+export async function checkMigrations(navPath) {
+    const needed = [];
+    for (const migration of MIGRATIONS) {
+        const check = await migration.check(navPath);
+        if (check.needed) {
+            needed.push({ migration, check });
+        }
+    }
+    return needed;
+}
+/**
+ * Apply a specific migration to a navigator
+ */
+export async function applyMigration(navPath, migration, confirm) {
+    return migration.apply(navPath, confirm);
+}
+/**
+ * Apply all needed migrations to a navigator
+ */
+export async function applyAllMigrations(navPath, confirm) {
+    const needed = await checkMigrations(navPath);
+    const results = [];
+    for (const { migration } of needed) {
+        const result = await applyMigration(navPath, migration, confirm);
+        results.push({ migration, result });
+        // Stop if a migration fails
+        if (!result.success) {
+            break;
+        }
+    }
+    const success = results.every(({ result }) => result.success);
+    return { results, success };
+}
+/**
+ * Get all available migrations
+ */
+export function getAllMigrations() {
+    return [...MIGRATIONS];
+}
+//# sourceMappingURL=index.js.map

package/dist/migrations/index.js.map

@@ -0,0 +1 @@
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package/dist/migrations/types.d.ts

@@ -0,0 +1,60 @@
+/**
+ * Migration system types
+ *
+ * Migrations bring existing navigators up to spec with latest best practices.
+ * Each migration is versioned, interactive, and safe.
+ */
+/**
+ * User confirmation function
+ * @param action - Brief description of the action
+ * @param details - Detailed explanation of what will change
+ * @returns Promise resolving to true if user confirms, false otherwise
+ */
+export type ConfirmFn = (action: string, details: string) => Promise<boolean>;
+/**
+ * Result of checking if a migration is needed
+ */
+export interface MigrationCheck {
+    /** Whether this migration is needed */
+    needed: boolean;
+    /** Human-readable reason why it's needed (or why not) */
+    reason: string;
+    /** Current version detected (if applicable) */
+    currentVersion?: string;
+}
+/**
+ * Result of applying a migration
+ */
+export interface MigrationResult {
+    /** Whether the migration succeeded */
+    success: boolean;
+    /** Human-readable message about what happened */
+    message: string;
+    /** List of files that were modified */
+    filesModified: string[];
+    /** List of errors encountered (if any) */
+    errors?: string[];
+}
+/**
+ * A migration that can be applied to a navigator
+ */
+export interface Migration {
+    /** Semver version this migration brings the navigator to */
+    version: string;
+    /** Human-readable description of what this migration does */
+    description: string;
+    /**
+     * Check if this migration is needed for the given navigator
+     * @param navPath - Absolute path to navigator directory
+     * @returns Check result indicating if migration is needed
+     */
+    check: (navPath: string) => Promise<MigrationCheck>;
+    /**
+     * Apply this migration to the given navigator
+     * @param navPath - Absolute path to navigator directory
+     * @param confirm - Function to ask user for confirmation before each change
+     * @returns Result of the migration
+     */
+    apply: (navPath: string, confirm: ConfirmFn) => Promise<MigrationResult>;
+}
+//# sourceMappingURL=types.d.ts.map

package/dist/migrations/types.d.ts.map

@@ -0,0 +1 @@
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package/dist/migrations/types.js

@@ -0,0 +1,8 @@
+/**
+ * Migration system types
+ *
+ * Migrations bring existing navigators up to spec with latest best practices.
+ * Each migration is versioned, interactive, and safe.
+ */
+export {};
+//# sourceMappingURL=types.js.map

package/dist/migrations/types.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"types.js","sourceRoot":"","sources":["../../src/migrations/types.ts"],"names":[],"mappings":"AAAA;;;;;GAKG"}

package/dist/migrations/versions/v1.3.1-submit-answer.d.ts

@@ -0,0 +1,20 @@
+/**
+ * Migration v1.3.1: Remove submit_answer Tool Instructions from CLAUDE.md
+ *
+ * This migration removes submit_answer tool instructions from CLAUDE.md templates.
+ * The submit_answer tool is an MCP tool that only exists when running via `autonav query`,
+ * not when running Claude Code TUI directly. Having these instructions in CLAUDE.md
+ * causes Claude to hallucinate the tool when running in TUI mode.
+ *
+ * The correct design:
+ * - CLAUDE.md: General grounding rules + response format guidelines (no tool mention)
+ * - autonav query prompt: Injects submit_answer requirement (tool only exists here)
+ *
+ * Changes:
+ * - Replaces "Response Format" section to remove submit_answer tool instructions
+ * - Updates section to focus on grounding and citation principles
+ * - Removes tool-specific examples
+ */
+import type { Migration } from "../types.js";
+export declare const migration: Migration;
+//# sourceMappingURL=v1.3.1-submit-answer.d.ts.map

package/dist/migrations/versions/v1.3.1-submit-answer.d.ts.map

@@ -0,0 +1 @@
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package/dist/migrations/versions/v1.3.1-submit-answer.js

@@ -0,0 +1,194 @@
+/**
+ * Migration v1.3.1: Remove submit_answer Tool Instructions from CLAUDE.md
+ *
+ * This migration removes submit_answer tool instructions from CLAUDE.md templates.
+ * The submit_answer tool is an MCP tool that only exists when running via `autonav query`,
+ * not when running Claude Code TUI directly. Having these instructions in CLAUDE.md
+ * causes Claude to hallucinate the tool when running in TUI mode.
+ *
+ * The correct design:
+ * - CLAUDE.md: General grounding rules + response format guidelines (no tool mention)
+ * - autonav query prompt: Injects submit_answer requirement (tool only exists here)
+ *
+ * Changes:
+ * - Replaces "Response Format" section to remove submit_answer tool instructions
+ * - Updates section to focus on grounding and citation principles
+ * - Removes tool-specific examples
+ */
+import * as fs from "node:fs";
+import * as path from "node:path";
+const MIGRATION_VERSION = "1.3.1";
+/**
+ * The new Response Format section without submit_answer tool mention
+ */
+const NEW_RESPONSE_FORMAT_SECTION = `## Response Format
+
+When answering questions, provide clear answers with proper citations:
+
+1. **Search first**: Use available tools to find relevant information
+2. **Cite sources**: Always reference specific files and sections where you found the information
+3. **Be grounded**: Only claim what's documented in the knowledge base
+4. **Acknowledge uncertainty**: If information is unclear or missing, say so explicitly
+
+### Source Citation Format
+
+Include inline citations in your answers:
+- Reference specific files: \`[deployment/ssl-config.md: SSL Configuration]\`
+- Quote relevant excerpts when helpful
+- Link conclusions to specific documentation
+
+### Confidence Assessment
+
+When uncertain about an answer:
+- **High confidence**: Information is explicit and well-documented
+- **Medium confidence**: Information requires some interpretation or combining sources
+- **Low confidence**: Information is sparse, unclear, or partially missing
+
+If your confidence is low, acknowledge the uncertainty and suggest that verification may be needed.`;
+/**
+ * Detect if CLAUDE.md has old submit_answer tool instructions
+ */
+function hasSubmitAnswerInstructions(claudeMdContent) {
+    // Check if CLAUDE.md mentions submit_answer tool
+    return claudeMdContent.includes('submit_answer');
+}
+/**
+ * Extract the section between two headers in markdown
+ */
+function extractSection(content, startHeader, endHeader) {
+    const lines = content.split('\n');
+    let startIndex = -1;
+    let endIndex = lines.length;
+    // Find start
+    for (let i = 0; i < lines.length; i++) {
+        const line = lines[i];
+        if (line && line.trim() === startHeader) {
+            startIndex = i;
+            break;
+        }
+    }
+    if (startIndex === -1) {
+        return null;
+    }
+    // Find end (next header of same or higher level, or specified header)
+    if (endHeader) {
+        for (let i = startIndex + 1; i < lines.length; i++) {
+            const line = lines[i];
+            if (line && line.trim() === endHeader) {
+                endIndex = i;
+                break;
+            }
+        }
+    }
+    else {
+        // Find next header of same or higher level
+        const startHeaderLevel = startHeader.match(/^#+/)?.[0].length || 2;
+        for (let i = startIndex + 1; i < lines.length; i++) {
+            const line = lines[i];
+            if (!line)
+                continue;
+            const headerMatch = line.match(/^(#+)\s/);
+            if (headerMatch && headerMatch[1] && headerMatch[1].length <= startHeaderLevel) {
+                endIndex = i;
+                break;
+            }
+        }
+    }
+    const sectionContent = lines.slice(startIndex, endIndex).join('\n');
+    const startPos = lines.slice(0, startIndex).join('\n').length + (startIndex > 0 ? 1 : 0);
+    const endPos = lines.slice(0, endIndex).join('\n').length + (endIndex > 0 ? 1 : 0);
+    return { content: sectionContent, startPos, endPos };
+}
+/**
+ * Check if this migration is needed
+ */
+async function check(navPath) {
+    const claudeMdPath = path.join(navPath, "CLAUDE.md");
+    if (!fs.existsSync(claudeMdPath)) {
+        return {
+            needed: false,
+            reason: "No CLAUDE.md file found",
+        };
+    }
+    const content = fs.readFileSync(claudeMdPath, "utf-8");
+    if (!hasSubmitAnswerInstructions(content)) {
+        return {
+            needed: false,
+            reason: "CLAUDE.md already updated (no submit_answer tool instructions)",
+        };
+    }
+    return {
+        needed: true,
+        reason: "CLAUDE.md contains submit_answer tool instructions that should be removed",
+    };
+}
+/**
+ * Apply the migration
+ */
+async function apply(navPath, confirm) {
+    const claudeMdPath = path.join(navPath, "CLAUDE.md");
+    const filesModified = [];
+    try {
+        const content = fs.readFileSync(claudeMdPath, "utf-8");
+        // Find the Response Format section and all related sections
+        // Extract from "## Response Format" to "## Remember" (new template) or end of file (old templates)
+        let section = extractSection(content, "## Response Format", "## Remember");
+        // If there's no "## Remember" section (old navigator), extract everything from Response Format onward
+        if (!section) {
+            section = extractSection(content, "## Response Format");
+        }
+        if (!section) {
+            return {
+                success: false,
+                message: "Could not find '## Response Format' section in CLAUDE.md",
+                filesModified,
+                errors: ["Missing '## Response Format' section"],
+            };
+        }
+        // Ask for confirmation
+        const confirmed = await confirm("Update Response Format section in CLAUDE.md", `This will remove submit_answer tool instructions from CLAUDE.md.\n\nThe submit_answer tool only exists when running via 'autonav query' and should not be mentioned in CLAUDE.md (which is read by all Claude Code sessions).\n\nOld section (${section.content.split('\n').length} lines) will be replaced with general response format guidelines.`);
+        if (!confirmed) {
+            return {
+                success: false,
+                message: "Migration cancelled by user",
+                filesModified,
+            };
+        }
+        // Replace the section
+        const newContent = content.substring(0, section.startPos) +
+            NEW_RESPONSE_FORMAT_SECTION +
+            content.substring(section.endPos);
+        // Write the updated content
+        fs.writeFileSync(claudeMdPath, newContent, "utf-8");
+        filesModified.push("CLAUDE.md");
+        // Update config.json version if it exists
+        const configPath = path.join(navPath, "config.json");
+        if (fs.existsSync(configPath)) {
+            const config = JSON.parse(fs.readFileSync(configPath, "utf-8"));
+            config.version = MIGRATION_VERSION;
+            fs.writeFileSync(configPath, JSON.stringify(config, null, 2) + "\n", "utf-8");
+            filesModified.push("config.json");
+        }
+        return {
+            success: true,
+            message: `Successfully updated to v${MIGRATION_VERSION}`,
+            filesModified,
+        };
+    }
+    catch (error) {
+        const errorMsg = error instanceof Error ? error.message : String(error);
+        return {
+            success: false,
+            message: `Migration failed: ${errorMsg}`,
+            filesModified,
+            errors: [errorMsg],
+        };
+    }
+}
+export const migration = {
+    version: MIGRATION_VERSION,
+    description: "Remove submit_answer tool instructions from CLAUDE.md",
+    check,
+    apply,
+};
+//# sourceMappingURL=v1.3.1-submit-answer.js.map

package/dist/migrations/versions/v1.3.1-submit-answer.js.map

@@ -0,0 +1 @@
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package/dist/skill-generator/index.d.ts.map

@@ -1 +1 @@
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package/dist/skill-generator/index.js

@@ -99,6 +99,15 @@ ${config.description}
 ${config.scope ? `**Scope**: ${config.scope}\n` : ""}
 ${config.audience ? `**Audience**: ${config.audience}\n` : ""}
 
+## Identity Protocol
+
+When querying this navigator, Claude Code should explicitly identify itself as the requester. This enables bidirectional identity affirmation and helps the navigator maintain context awareness.
+
+**Example**:
+\`\`\`bash
+autonav query "${navPath}" "Claude Code here, asking: How do I deploy?"
+\`\`\`
+
 ## How to Use
 
 Simply use \`autonav query\` to ask questions:

package/dist/skill-generator/index.js.map

@@ -1 +1 @@
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package/dist/templates/CLAUDE-pack.md.template

@@ -21,6 +21,11 @@ When answering questions:
 
 Always structure responses with proper source citations as specified in `system-configuration.md`.
 
+**IMPORTANT**: When citing sources in the `submit_answer` tool:
+- Use ONLY the filename (e.g., "planting.md"), NOT the full path (NOT "knowledge/planting.md")
+- The knowledge base directory is already known to be `knowledge/`
+- Example: `file: "planting.md"` ✓   NOT `file: "knowledge/planting.md"` ✗
+
 Include:
 - Direct answer
 - File path references: [filename.md: Section Heading]
@@ -29,4 +34,10 @@ Include:
 
 ## Response Format
 
-Follow the response format guidelines in `system-configuration.md`. Always use structured JSON responses following the NavigatorResponse schema.
+The `system-configuration.md` file provides detailed response guidelines for this knowledge pack.
+
+Key principles:
+- Always cite specific sources from the knowledge base
+- Be explicit about confidence levels
+- Acknowledge when information is missing or uncertain
+- Follow any domain-specific formatting rules in `system-configuration.md`

package/dist/templates/CLAUDE.md.template

@@ -52,72 +52,28 @@ You MUST follow these rules when answering questions:
 
 ## Response Format
 
-Always structure your responses as JSON following the NavigatorResponse schema:
-
-```json
-{
-  "protocolVersion": "1.0.0",
-  "query": "the question asked",
-  "answer": "your detailed answer with inline citations",
-  "sources": [
-    {
-      "filePath": "relative/path/from/knowledge-base/file.md",
-      "excerpt": "exact quote from the file",
-      "section": "section heading"
-    }
-  ],
-  "confidence": 0.95
-}
-```
-
-## Example: Good Response
-
-**Question**: "How do I configure SSL?"
-
-```json
-{
-  "protocolVersion": "1.0.0",
-  "query": "How do I configure SSL?",
-  "answer": "To configure SSL, you need to update the load balancer settings. According to deployment/ssl-config.md, you should set the certificate ARN in the Terraform configuration.",
-  "sources": [
-    {
-      "filePath": "deployment/ssl-config.md",
-      "excerpt": "Set the certificate_arn parameter in the aws_lb_listener resource",
-      "section": "SSL Configuration"
-    }
-  ],
-  "confidence": 0.95
-}
-```
-
-## Example: Bad Response (Don't do this)
-
-**Question**: "How do I configure SSL?"
-
-```json
-{
-  "query": "How do I configure SSL?",
-  "answer": "You can configure SSL by updating the config.yaml file and setting ssl_enabled to true.",
-  "sources": [],
-  "confidence": 0.8
-}
-```
-
-**Problems**:
-- No sources cited
-- File path (config.yaml) may not exist
-- Vague answer without specifics
-- Claims knowledge without evidence
-
-## Confidence Scoring Guide
-
-- **1.0**: Fully grounded, multiple authoritative sources, no ambiguity
-- **0.8-0.9**: Well grounded, clear sources, minor gaps
-- **0.6-0.7**: Partially grounded, some inference required
-- **0.4-0.5**: Weakly grounded, significant uncertainty
-- **0.0-0.3**: Not grounded, likely needs human review
-
-If your confidence is below 0.5, acknowledge the uncertainty in your answer and suggest that a human review may be needed.
+When answering questions, provide clear answers with proper citations:
+
+1. **Search first**: Use available tools to find relevant information
+2. **Cite sources**: Always reference specific files and sections where you found the information
+3. **Be grounded**: Only claim what's documented in the knowledge base
+4. **Acknowledge uncertainty**: If information is unclear or missing, say so explicitly
+
+### Source Citation Format
+
+Include inline citations in your answers:
+- Reference specific files: `[deployment/ssl-config.md: SSL Configuration]`
+- Quote relevant excerpts when helpful
+- Link conclusions to specific documentation
+
+### Confidence Assessment
+
+When uncertain about an answer:
+- **High confidence**: Information is explicit and well-documented
+- **Medium confidence**: Information requires some interpretation or combining sources
+- **Low confidence**: Information is sparse, unclear, or partially missing
+
+If your confidence is low, acknowledge the uncertainty and suggest that verification may be needed.
 
 ## Remember