refactor(examples): restructure Python examples with dedicated directories

- Remove old advanced.py and custom_config.py files
- Add new example structure with dedicated directories for basic,
  advanced, and custom_config examples
- Each example now has its own README.md, main.py, and pyproject.toml
- Update basic example to use from_content instead of from_text
- Add proper configuration examples and documentation

fix(python): improve IndexContext and Engine class naming

- Rename from_text to from_content for better semantic meaning
- Add explicit class names for Python bindings (IndexContext,
  QueryResult, DocumentInfo, Engine)
- Update error handling with proper constructor
- Fix module name from _vectorless to vectorless

refactor(rust): update document format handling and builder logic

- Remove Text format support temporarily
- Set default format to Markdown instead of Text
- Fix EngineBuilder to properly handle API key and model precedence
- Update with_openai to not override existing model configuration
- Improve documentation for builder methods

Author: zTgx

examples/python/advanced.py

@@ -0,0 +1,45 @@
+# Advanced Example - Full Configuration
+
+Use a configuration file for fine-grained control.
+
+## Setup
+
+```bash
+pip install vectorless
+
+# Copy the example config
+cp ../../../config.toml ./vectorless.toml
+
+# Edit to customize your settings
+vim vectorless.toml
+```
+
+## Run
+
+```bash
+python main.py
+```
+
+## Configuration File Structure
+
+```toml
+[llm]
+api_key = "sk-..."
+
+[llm.summary]
+model = "gpt-4o-mini"
+max_tokens = 200
+
+[llm.retrieval]
+model = "gpt-4o"
+max_tokens = 100
+
+[retrieval]
+top_k = 5
+beam_width = 3
+max_iterations = 10
+
+[storage]
+workspace_dir = "./workspace"
+cache_size = 100
+```

examples/python/advanced/README.md

@@ -0,0 +1,115 @@
+#!/usr/bin/env python3
+"""
+Advanced example - Full Configuration File.
+
+This example demonstrates how to use a full configuration file
+for fine-grained control over all settings.
+
+Usage:
+    cp ../../../config.toml ./vectorless.toml
+    # Edit vectorless.toml to customize settings
+    python main.py
+"""
+
+import os
+from vectorless import Engine, IndexContext
+
+# Path to config file (relative to this script)
+CONFIG_PATH = "./vectorless.toml"
+WORKSPACE = "./workspace"
+
+
+def main():
+    print("=== Vectorless Advanced Example (Full Configuration) ===\n")
+
+    # Check if config file exists
+    if not os.path.exists(CONFIG_PATH):
+        print(f"Error: Config file not found: {CONFIG_PATH}")
+        print("\nCreate it by copying the example:")
+        print(f"  cp ../../../config.toml {CONFIG_PATH}")
+        print("\nThen edit it to customize your settings.")
+        return
+
+    # Create engine with config file
+    engine = Engine(config_path=CONFIG_PATH)
+
+    print(f"✓ Engine created with config file: {CONFIG_PATH}\n")
+
+    # Index a document
+    content = """
+# System Documentation
+
+## Architecture
+
+The system consists of three main components:
+
+1. **Index Pipeline** - Parses documents and builds a navigable tree
+2. **Retrieval Pipeline** - Queries and retrieves relevant content
+3. **Pilot** - LLM-powered navigation guide
+
+## Configuration Options
+
+### LLM Settings
+- `model`: The LLM model to use (e.g., "gpt-4o", "gpt-4o-mini")
+- `endpoint`: API endpoint URL
+- `api_key`: Your API key
+- `temperature`: Generation temperature (0.0 for deterministic)
+
+### Retrieval Settings
+- `top_k`: Number of results to return
+- `max_iterations`: Maximum search iterations
+- `beam_width`: Beam width for multi-path search
+
+### Storage Settings
+- `workspace_dir`: Directory for persisted documents
+- `cache_size`: LRU cache size
+- `compression`: Enable/disable compression
+
+## Performance Tuning
+
+For faster retrieval:
+- Use a smaller model like gpt-4o-mini
+- Reduce max_iterations
+- Enable caching
+
+For higher accuracy:
+- Use a more capable model like gpt-4o
+- Increase beam_width
+- Enable multi-turn decomposition
+"""
+    ctx = IndexContext.from_content(content, name="system_docs", format="markdown")
+    doc_id = engine.index(ctx)
+    print(f"✓ Indexed: {doc_id}\n")
+
+    # Query examples
+    questions = [
+        "What are the main components?",
+        "How can I improve retrieval speed?",
+        "What settings are available?",
+    ]
+
+    for q in questions:
+        result = engine.query(doc_id, q)
+        print(f"Q: {q}")
+        print(f"A: {result.content[:150]}...")
+        print(f"   Score: {result.score:.2f}\n")
+
+    # Cleanup
+    engine.remove(doc_id)
+    print("✓ Cleaned up")
+
+    # Print configuration info
+    print("\n" + "=" * 60)
+    print("Configuration Priority")
+    print("=" * 60)
+    print("""
+1. Default configuration
+2. Auto-detected config file (vectorless.toml, config.toml)
+3. Explicit config file (config_path parameter)
+4. Environment variables (OPENAI_API_KEY, etc.)
+5. Constructor parameters (api_key, model, etc.)
+""")
+
+
+if __name__ == "__main__":
+    main()

examples/python/advanced/main.py

@@ -0,0 +1,11 @@
+[project]
+name = "vectorless-advanced-example"
+version = "0.1.0"
+requires-python = ">=3.9"
+dependencies = [
+    "vectorless",
+]
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"

examples/python/advanced/pyproject.toml

@@ -0,0 +1,16 @@
+# Basic Example - Zero Configuration
+
+The simplest way to use Vectorless.
+
+## Setup
+
+```bash
+pip install vectorless
+export OPENAI_API_KEY="sk-..."
+```
+
+## Run
+
+```bash
+python main.py
+```

examples/python/basic/README.md

@@ -1,16 +1,13 @@
 #!/usr/bin/env python3
-# Copyright (c) 2026 vectorless developers
-# SPDX-License-Identifier: Apache-2.0
-
 """
-Basic usage example - Zero Configuration.
+Basic example - Zero Configuration.
 
 This example demonstrates the simplest way to use Vectorless.
 Just set OPENAI_API_KEY environment variable and you're ready to go.
 
 Usage:
     export OPENAI_API_KEY="sk-..."
-    python basic.py
+    python main.py
 """
 
 import os
@@ -22,7 +19,6 @@ def main():
     print("=== Vectorless Basic Example (Zero Configuration) ===\n")
 
     # Zero configuration: Just set OPENAI_API_KEY environment variable
-    # The engine will automatically use it.
     with tempfile.TemporaryDirectory() as workspace:
         engine = Engine(workspace=workspace)
 
@@ -56,7 +52,7 @@ def main():
 print(result.content)
 ```
 """
-        ctx = IndexContext.from_text(content, name="manual", format="markdown")
+        ctx = IndexContext.from_content(content, name="manual", format="markdown")
         doc_id = engine.index(ctx)
         print(f"✓ Indexed: {doc_id}\n")
 

examples/python/basic.py examples/python/basic/main.pyexamples/python/basic.py renamed to examples/python/basic/main.py

@@ -0,0 +1,11 @@
+[project]
+name = "vectorless-basic-example"
+version = "0.1.0"
+requires-python = ">=3.9"
+dependencies = [
+    "vectorless",
+]
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"