Deep link to markdown entries by line number in uri

Use url fragment schema for deep link URIs, borrowing from URL/PDF
schemas. E.g file:///path/to/file.txt#line=<line_no>&#page=<page_no>

Compute line number during (recursive) markdown entry chunking.

Test line number in URI maps to line number of chunk in actual md file.

This deeplink URI with line number is passed to llm as context to
better combine with line range based view file tool.

Grep tool already passed matching line number. This change passes
line number in URIs of markdown entries matched by the semantic search
tool.

tests/data/markdown/main_readme.md

@@ -0,0 +1,39 @@
+# Main Readme
+> Allow natural language search, chat with your documents using transformer based models
+
+This is a test markdown file with multiple, nested child entries.
+
+## Dependencies
+
+- Python3
+- [Miniconda](https://docs.conda.io/en/latest/miniconda.html#latest-miniconda-installer-links)
+
+## Installation
+
+```bash
+pip install khoj
+```
+
+## Run
+  Load ML model, generate embeddings and expose API to query specified org-mode files
+
+  ```shell
+  python3 main.py --input-files ~/Notes/Schedule.org ~/Notes/Incoming.org --verbose
+  ```
+
+## Use
+
+### **Khoj via API**
+- Query: `GET` [http://localhost:42110/api/search?q="What is the meaning of life"](http://localhost:42110/api/search?q=%22what%20is%20the%20meaning%20of%20life%22)
+- Update Index: `GET` [http://localhost:42110/api/update](http://localhost:42110/api/update)
+- [Khoj API Docs](http://localhost:42110/docs)
+
+### *Khoj via Web*
+
+- Open browser to http://localhost:42110
+- Enter query in search box
+
+## Acknowledgments
+
+- [MiniLM Model](https://huggingface.co/sentence-transformers/multi-qa-MiniLM-L6-cos-v1) for Asymmetric Text Search. See (SBert Documentation)[https://www.sbert.net/examples/applications/retrieve_rerank/README.html]
+- [OpenAI CLIP Model](https://github.com/openai/CLIP) for Image Search. See [SBert Documentation](https://www.sbert.net/examples/applications/image-search/README.html)

tests/test_markdown_to_entries.py

@@ -1,4 +1,5 @@
 import os
+import re
 from pathlib import Path
 
 from khoj.processor.content.markdown.markdown_to_entries import MarkdownToEntries
@@ -248,6 +249,58 @@ def test_get_markdown_files(tmp_path):
     assert set(extracted_org_files.keys()) == expected_files
 
 
+def test_line_number_tracking_in_recursive_split():
+    "Ensure line numbers in URIs are correct after recursive splitting by checking against the actual file."
+    # Arrange
+    markdown_file_path = os.path.abspath("tests/data/markdown/main_readme.md")
+
+    with open(markdown_file_path, "r") as f:
+        markdown_content = f.read()
+    lines = markdown_content.splitlines()
+    data = {markdown_file_path: markdown_content}
+
+    # Act
+    # Using a small max_tokens to force recursive splitting
+    _, entries = MarkdownToEntries.extract_markdown_entries(markdown_files=data, max_tokens=10)
+
+    # Assert
+    assert len(entries) > 0, "No entries were extracted."
+
+    for entry in entries:
+        # Extract file path and line number from the entry URI
+        # for files uri is expected in format: file:///path/to/file.md#line=5
+        match = re.search(r"file://(.*?)#line=(\d+)", entry.uri)
+        filepath_from_uri = match.group(1)
+        line_number_from_uri = int(match.group(2))
+
+        # line_number is 1-based, list index is 0-based
+        line_in_file = clean(lines[line_number_from_uri - 1])
+        next_line_in_file = clean(lines[line_number_from_uri]) if line_number_from_uri < len(lines) else ""
+
+        # Remove ancestor heading lines inserted during post-processing
+        first_entry_line = ""
+        for line in entry.raw.splitlines():
+            if line.startswith("#"):
+                first_entry_line = line
+            else:
+                break  # Stop at the first non-heading line
+        # Remove heading prefix from entry.compiled as level changed during post-processing
+        cleaned_first_entry_line = first_entry_line.strip()
+        # Remove multiple consecutive spaces
+        cleaned_first_entry_line = clean(cleaned_first_entry_line)
+
+        assert entry.uri is not None, f"Entry '{entry}' has a None URI."
+        assert match is not None, f"URI format is incorrect: {entry.uri}"
+        assert (
+            filepath_from_uri == markdown_file_path
+        ), f"File path in URI '{filepath_from_uri}' does not match expected '{markdown_file_path}'"
+
+        # Ensure the first non-heading line in the compiled entry matches the line in the file
+        assert (
+            cleaned_first_entry_line in line_in_file.strip() or cleaned_first_entry_line in next_line_in_file.strip()
+        ), f"First non-heading line '{cleaned_first_entry_line}' in {entry.raw} does not match line {line_number_from_uri} in file: '{line_in_file}' or next line '{next_line_in_file}'"
+
+
 # Helper Functions
 def create_file(tmp_path: Path, entry=None, filename="test.md"):
     markdown_file = tmp_path / filename
@@ -255,3 +308,8 @@ def create_file(tmp_path: Path, entry=None, filename="test.md"):
     if entry:
         markdown_file.write_text(entry)
     return markdown_file
+
+
+def clean(text):
+    "Normalize spaces in text for easier comparison."
+    return re.sub(r"\s+", " ", text)