obsidian-mcp: rename edit_document -> replace_document_content; add line-granular tools (read/insert/replace_document_lines)

server.py

@@ -3,15 +3,25 @@ Obsidian MCP Server — Expose Obsidian vaults as MCP tools.
 
 Transport: StreamableHTTP (reachable cross-OS from WSL2 to Windows host).
 Run: python server.py --vaults-root "D:\\Obsidian" --port 8765
+
+v3.1 — Git sync + auto-embedding:
+  - READ tools: git pull (2-min debounce) before accessing vault files
+  - WRITE tools: embed content via bge-micro-v2, write .smart-env/multi/*.ajson, git push
+  - smart-connections MCP auto-detects ajson changes via maybeReload()
 """
 
 from __future__ import annotations
 
 import argparse
+import datetime as dt
 import json
 import os
 import re
-from datetime import datetime, timezone
+import subprocess
+import sys
+import threading
+import time
+from datetime import timezone
 from pathlib import Path
 from typing import Any
 
@@ -46,12 +56,198 @@ DEFAULT_EXCLUDE_EXT = {".webp", ".png", ".jpg", ".jpeg", ".gif", ".svg",
                        ".pdf", ".mp4", ".mp3", ".mov", ".excalidraw", ".bmp",
                        ".ico", ".tiff", ".heic", ".avif"}
 
+# ── Git Sync ───────────────────────────────────────────────────────────────
+
+_git_lock = threading.Lock()
+_last_git_pull: dict[str, float] = {}   # vault_path -> timestamp
+GIT_PULL_DEBOUNCE_S = 120
+
+
+def _git_pull_if_stale(vault_path: Path) -> None:
+    """Pull latest changes if last pull was > GIT_PULL_DEBOUNCE_S ago."""
+    key = str(vault_path)
+    now = time.time()
+    if now - _last_git_pull.get(key, 0) < GIT_PULL_DEBOUNCE_S:
+        return
+
+    git_dir = vault_path / ".git"
+    if not git_dir.is_dir():
+        return
+
+    with _git_lock:
+        # Re-check inside lock
+        if now - _last_git_pull.get(key, 0) < GIT_PULL_DEBOUNCE_S:
+            return
+        try:
+            subprocess.run(
+                ["git", "pull", "--ff-only"],
+                cwd=vault_path,
+                capture_output=True,
+                timeout=30,
+                check=False,
+            )
+        except (subprocess.TimeoutExpired, OSError):
+            pass
+        _last_git_pull[key] = time.time()
+
+
+def _git_commit_and_push(vault_path: Path, msg: str) -> None:
+    """Stage all changes, commit, and push."""
+    git_dir = vault_path / ".git"
+    if not git_dir.is_dir():
+        return
+
+    with _git_lock:
+        try:
+            subprocess.run(
+                ["git", "add", "-A"],
+                cwd=vault_path,
+                capture_output=True,
+                timeout=30,
+                check=False,
+            )
+            subprocess.run(
+                ["git", "commit", "-m", msg, "--allow-empty"],
+                cwd=vault_path,
+                capture_output=True,
+                timeout=30,
+                check=False,
+            )
+            subprocess.run(
+                ["git", "push"],
+                cwd=vault_path,
+                capture_output=True,
+                timeout=60,
+                check=False,
+            )
+        except (subprocess.TimeoutExpired, OSError):
+            pass
+
+
+# ── Embedding (Smart Connections ajson format) ─────────────────────────────
+
+_embed_model = None
+_embed_lock = threading.Lock()
+EMBED_MODEL_KEY = "TaylorAI/bge-micro-v2"
+
+
+def _get_embedder():
+    """Lazy-load bge-micro-v2. Returns tuple (model, dim)."""
+    global _embed_model
+    if _embed_model is not None:
+        return _embed_model
+
+    with _embed_lock:
+        if _embed_model is not None:
+            return _embed_model
+        try:
+            import numpy as np
+            from sentence_transformers import SentenceTransformer
+            model = SentenceTransformer(EMBED_MODEL_KEY)
+            dim = model.get_sentence_embedding_dimension()
+            _embed_model = (model, dim)
+            return _embed_model
+        except ImportError:
+            return None
+        except Exception:
+            return None
+
+
+def _ajson_filename(doc_path: str) -> str:
+    """Convert doc path to ajson filename: '01 - Sessions/Session 01.md' -> '01 - Sessions_Session 01_md.ajson'"""
+    return doc_path.replace("/", "_").replace(".md", "_md") + ".ajson"
+
+
+def _ajson_path(vault_path: Path, doc_path: str) -> Path:
+    """Get the full path to the ajson file for a note."""
+    return vault_path / ".smart-env" / "multi" / _ajson_filename(doc_path)
+
+
+def _write_ajson_entry(vault_path: Path, doc_path: str, content: str) -> bool:
+    """Embed note content and write/update its .smart-env/multi/*.ajson file.
+
+    Returns True on success, False on failure (embedding unavailable, etc.)
+    """
+    result = _get_embedder()
+    if result is None:
+        return False
+
+    model, dim = result
+    try:
+        import numpy as np
+        vec = model.encode(content, normalize_embeddings=True)
+        vec_list = [float(v) for v in vec.tolist()]
+    except Exception:
+        return False
+
+    entry = {
+        f"smart_sources:{doc_path}": {
+            "path": doc_path,
+            "embeddings": {
+                EMBED_MODEL_KEY: {"vec": vec_list}
+            },
+        }
+    }
+
+    ajson_file = _ajson_path(vault_path, doc_path)
+    ajson_file.parent.mkdir(parents=True, exist_ok=True)
+
+    # Write: one JSON object per line (append-compatible, but we overwrite
+    # the whole file for simplicity — it's one note per file)
+    line = json.dumps(entry)[1:-1] + ",\n"  # strip outer {}, add trailing comma+newline
+    ajson_file.write_text(line, encoding="utf-8")
+    return True
+
+
+def _delete_ajson_entry(vault_path: Path, doc_path: str) -> bool:
+    """Remove a note's ajson file from .smart-env/multi/. Returns True if deleted."""
+    ajson_file = _ajson_path(vault_path, doc_path)
+    if ajson_file.exists():
+        ajson_file.unlink()
+        return True
+    return False
+
+
+# ── Sync hooks ─────────────────────────────────────────────────────────────
+
+def _sync_pre_read(vault_name: str) -> None:
+    """Called before any read tool. Pulls git if stale."""
+    try:
+        vault = _vault_path(vault_name)
+        _git_pull_if_stale(vault)
+    except (ValueError, FileNotFoundError, NotADirectoryError):
+        pass
+
+
+def _sync_post_write(vault_name: str, doc_path: str, content: str | None = None) -> None:
+    """Called after any write tool. Embeds + pushes via git."""
+    try:
+        vault = _vault_path(vault_name)
+    except (ValueError, FileNotFoundError, NotADirectoryError):
+        return
+
+    if content is not None:
+        _write_ajson_entry(vault, doc_path, content)
+
+    _git_commit_and_push(vault, f"[hermes] auto-sync: {doc_path}")
+
+
+def _sync_post_delete(vault_name: str, doc_path: str) -> None:
+    """Called after delete_document. Removes ajson + pushes."""
+    try:
+        vault = _vault_path(vault_name)
+    except (ValueError, FileNotFoundError, NotADirectoryError):
+        return
+
+    _delete_ajson_entry(vault, doc_path)
+    _git_commit_and_push(vault, f"[hermes] auto-sync: delete {doc_path}")
+
 
 # ── Helpers ───────────────────────────────────────────────────────────────
 
 def _compact_date(timestamp: float) -> str:
     """Return YYYY-MM-DD (no time/microseconds/tz — 1/10 the token cost)."""
-    return datetime.fromtimestamp(timestamp, tz=timezone.utc).strftime("%Y-%m-%d")
+    return dt.datetime.fromtimestamp(timestamp, tz=timezone.utc).strftime("%Y-%m-%d")
 
 
 def _is_hidden_path(rel: Path) -> bool:
@@ -62,26 +258,63 @@ def _is_hidden_path(rel: Path) -> bool:
 # ── Helpers ───────────────────────────────────────────────────────────────
 
 def _vault_path(vault_name: str) -> Path:
-    """Get the absolute path to a vault directory, with safety check."""
+    """Get the absolute path to a vault directory, with safety check.
+
+    Falls back to case-insensitive matching if the exact name isn't found.
+    """
     vault = (VAULTS_ROOT / vault_name).resolve()
     # Ensure it's actually inside VAULTS_ROOT (prevent traversal)
     if not str(vault).startswith(str(VAULTS_ROOT.resolve())):
         raise ValueError(f"Vault name escapes root: {vault_name}")
+
     if not vault.exists():
-        raise FileNotFoundError(f"Vault not found: {vault_name}")
+        # Case-insensitive fallback: scan siblings at the same level
+        parent = vault.parent
+        lower = vault_name.lower()
+        for candidate in parent.iterdir():
+            if candidate.is_dir() and candidate.name.lower() == lower:
+                vault = candidate.resolve()
+                break
+        else:
+            raise FileNotFoundError(f"Vault not found: {vault_name}")
+
     if not vault.is_dir():
         raise NotADirectoryError(f"Not a directory: {vault_name}")
     return vault
 
 
 def _resolve_doc(vault_name: str, doc_path: str) -> Path:
-    """Resolve a document path within a vault, preventing traversal."""
+    """Resolve a document path within a vault, preventing traversal.
+
+    Falls back to case-insensitive path component matching on Linux.
+    """
     vault = _vault_path(vault_name)
     # Normalize: strip leading slash, handle backslashes
     clean = doc_path.lstrip("/\\").replace("\\", "/")
     target = (vault / clean).resolve()
     if not str(target).startswith(str(vault)):
         raise ValueError(f"Document path escapes vault: {doc_path}")
+
+    if not target.exists():
+        # Case-insensitive path component fallback
+        parts = clean.split("/")
+        current = vault
+        for part in parts:
+            lower = part.lower()
+            found = None
+            for child in current.iterdir():
+                if child.name.lower() == lower:
+                    found = child
+                    break
+            if found is None:
+                # Component not found — let the original target raise
+                break
+            current = found
+        else:
+            # All components resolved case-insensitively
+            if str(current.resolve()).startswith(str(vault)):
+                return current.resolve()
+
     return target
 
 
@@ -104,7 +337,7 @@ def _file_info_full(p: Path, relative_to: Path) -> dict[str, Any]:
         "size_bytes": stat.st_size if p.is_file() else None,
         "modified": _compact_date(stat.st_mtime),
     }
-    if p.is_file() and _is_markdown(p):
+    if p.is_file() and isinstance(info, dict):
         try:
             content = p.read_text(encoding="utf-8", errors="replace")
         except Exception:
@@ -118,29 +351,6 @@ def _is_markdown(p: Path) -> bool:
     return p.suffix.lower() in MARKDOWN_EXT
 
 
-def _search_file(filepath: Path, query: str) -> list[dict[str, Any]]:
-    """Search a single markdown file for query, return match contexts."""
-    try:
-        text = filepath.read_text(encoding="utf-8", errors="replace")
-    except Exception:
-        return []
-    results = []
-    query_lower = query.lower()
-    for i, line in enumerate(text.splitlines(), start=1):
-        if query_lower in line.lower():
-            # Trim context snippet
-            idx = line.lower().index(query_lower)
-            start = max(0, idx - 40)
-            end = min(len(line), idx + len(query) + 40)
-            snippet = line[start:end]
-            if start > 0:
-                snippet = "…" + snippet
-            if end < len(line):
-                snippet += "…"
-            results.append({"line": i, "snippet": snippet.strip()})
-    return results
-
-
 def _parse_wikilinks(content: str) -> list[str]:
     """Extract [[wikilink]] targets from markdown content."""
     # Match [[Target]] or [[Target|Alias]]
@@ -230,6 +440,7 @@ def list_vault(
         total: combined count
     """
     vault = _vault_path(vault_name)
+    _sync_pre_read(vault_name)
     # Normalize the inner path
     clean_path = path.lstrip("/\\").replace("\\", "/")
     target = (vault / clean_path).resolve() if clean_path else vault
@@ -296,6 +507,7 @@ def get_vault_document(vault_name: str, doc_path: str) -> dict[str, Any]:
 
     Returns the document content with metadata.
     """
+    _sync_pre_read(vault_name)
     target = _resolve_doc(vault_name, doc_path)
     if not target.exists():
         return {"error": f"Document not found: {doc_path}", "vault": vault_name}
@@ -329,56 +541,13 @@ def get_file_info(vault_name: str, doc_path: str) -> dict[str, Any]:
     Returns metadata dict with: name, path, type, size_bytes, modified (YYYY-MM-DD),
     and for markdown files: line_count, char_count.
     """
+    _sync_pre_read(vault_name)
     target = _resolve_doc(vault_name, doc_path)
     if not target.exists():
         return {"error": f"File not found: {doc_path}", "vault": vault_name}
     return _file_info_full(target, _vault_path(vault_name))
 
 
-@mcp.tool()
-def search_vault(vault_name: str, query: str, max_results: int = 50) -> dict[str, Any]:
-    """FILESYSTEM TOOL (not memory) — Search markdown files on disk. Find notes about characters, locations, concepts.
-
-    Args:
-        vault_name: Name of the vault to search.
-        query: Search query (case-insensitive substring match).
-        max_results: Maximum number of match results to return (default 50).
-
-    Returns matches grouped by file with line numbers and context snippets.
-    """
-    vault = _vault_path(vault_name)
-    results = []
-    files_searched = 0
-
-    for md_file in vault.rglob("*.md"):
-        rel_path = md_file.relative_to(vault)
-        if _is_hidden_path(rel_path):
-            continue
-
-        files_searched += 1
-        matches = _search_file(md_file, query)
-        if matches:
-            results.append({
-                "file": str(rel_path).replace("\\", "/"),
-                "matches": matches[:max_results],
-                "match_count": len(matches),
-            })
-
-        if len(results) >= max_results:
-            break
-
-    # Sort by match count descending
-    results.sort(key=lambda r: r["match_count"], reverse=True)
-
-    return {
-        "vault": vault_name,
-        "query": query,
-        "results": results[:max_results],
-        "total_matches": sum(r["match_count"] for r in results),
-        "files_searched": files_searched,
-        "files_with_matches": len(results),
-    }
-
 
 @mcp.tool()
 def get_recent_changes(vault_name: str, limit: int = 20) -> dict[str, Any]:
@@ -390,6 +559,7 @@ def get_recent_changes(vault_name: str, limit: int = 20) -> dict[str, Any]:
 
     Returns documents sorted by modification time, most recent first.
     """
+    _sync_pre_read(vault_name)
     vault = _vault_path(vault_name)
     md_files = []
 
@@ -423,6 +593,7 @@ def get_backlinks(vault_name: str, doc_path: str) -> dict[str, Any]:
 
     Returns a list of files that link to it, with context snippets.
     """
+    _sync_pre_read(vault_name)
     vault = _vault_path(vault_name)
     target = _resolve_doc(vault_name, doc_path)
     target_rel = str(target.relative_to(vault)).replace("\\", "/")
@@ -447,8 +618,9 @@ def get_backlinks(vault_name: str, doc_path: str) -> dict[str, Any]:
         matching_links = []
         for m in pattern.finditer(content):
             link_target = m.group(1).strip()
-            # Match if link_target matches stem, filename, or full path
-            if link_target == target_stem or link_target == target_rel or link_target == target.name:
+            # Case-insensitive match against stem, filename, or full path
+            link_lower = link_target.lower()
+            if link_lower == target_stem.lower() or link_lower == target_rel.lower() or link_lower == target.name.lower():
                 # Get line context
                 line_no = content[:m.start()].count("\n") + 1
                 lines = content.splitlines()
@@ -485,6 +657,7 @@ def create_document(vault_name: str, doc_path: str, content: str) -> dict[str, A
 
     Returns the created document info.
     """
+    _sync_pre_read(vault_name)
     if not doc_path.lower().endswith(".md"):
         doc_path = doc_path.rstrip("/\\") + ".md"
 
@@ -495,25 +668,33 @@ def create_document(vault_name: str, doc_path: str, content: str) -> dict[str, A
     target.parent.mkdir(parents=True, exist_ok=True)
     target.write_text(content, encoding="utf-8")
 
+    # Sync
+    clean_path = doc_path.lstrip("/\\").replace("\\", "/")
+    _sync_post_write(vault_name, clean_path, content)
+
     return {
         "vault": vault_name,
-        "path": doc_path.lstrip("/\\").replace("\\", "/"),
+        "path": clean_path,
         "action": "created",
         "size_bytes": target.stat().st_size,
     }
 
 
 @mcp.tool()
-def edit_document(vault_name: str, doc_path: str, content: str) -> dict[str, Any]:
-    """Edit (overwrite) an existing markdown document in a vault.
+def replace_document_content(vault_name: str, doc_path: str, content: str) -> dict[str, Any]:
+    """REPLACES THE ENTIRE FILE with `content` — this is a full overwrite, NOT a
+    patch or partial edit. Pass the COMPLETE new document text, not a fragment.
+    If you only need to add text at the end, use append_to_document. If you need
+    to change a few lines in place, use replace_document_lines or insert_document_lines.
 
     Args:
         vault_name: Name of the vault.
         doc_path: Relative path to the document.
-        content: New markdown content (replaces entire file).
+        content: COMPLETE new markdown content for the whole document.
 
-    Returns the edited document info.
+    Returns the replaced document info.
     """
+    _sync_pre_read(vault_name)
     if not doc_path.lower().endswith(".md"):
         doc_path = doc_path.rstrip("/\\") + ".md"
 
@@ -523,14 +704,235 @@ def edit_document(vault_name: str, doc_path: str, content: str) -> dict[str, Any
 
     target.write_text(content, encoding="utf-8")
 
+    # Sync
+    clean_path = doc_path.lstrip("/\\").replace("\\", "/")
+    _sync_post_write(vault_name, clean_path, content)
+
+    return {
+        "vault": vault_name,
+        "path": clean_path,
+        "action": "replaced",
+        "size_bytes": target.stat().st_size,
+    }
+
+
+@mcp.tool()
+def read_document_lines(vault_name: str, doc_path: str, starting_line_number: int, total_lines: int) -> dict[str, Any]:
+    """Read a bounded window of lines from a markdown document.
+
+    Lines are 1-indexed. `starting_line_number` is the first line returned;
+    `total_lines` is the number of lines to return. Returns the full document's
+    `total_lines` count so callers can page through a large note in chunks.
+
+    Args:
+        vault_name: Name of the vault.
+        doc_path: Relative path to the document.
+        starting_line_number: 1-indexed line to start reading from (>= 1).
+        total_lines: Number of lines to return.
+
+    Returns the line window plus the document's total line count.
+    """
+    _sync_pre_read(vault_name)
+    target = _resolve_doc(vault_name, doc_path)
+    if not target.exists():
+        return {"error": f"Document not found: {doc_path}", "vault": vault_name}
+
+    content = target.read_text(encoding="utf-8", errors="replace")
+    lines = content.splitlines()
+    line_count = len(lines)
+
+    start = max(1, starting_line_number)
+    end = start + max(0, total_lines)
+    window = lines[start - 1 : end]
+
     return {
         "vault": vault_name,
         "path": doc_path.lstrip("/\\").replace("\\", "/"),
-        "action": "edited",
+        "content": "\n".join(window),
+        "starting_line_number": start,
+        "returned_lines": len(window),
+        "total_lines": line_count,
+    }
+
+
+@mcp.tool()
+def insert_document_lines(vault_name: str, doc_path: str, starting_line_number: int, new_content: str) -> dict[str, Any]:
+    """Insert lines into a markdown document at a specific position.
+
+    1-indexed, insert-AT semantics: `new_content`'s first line lands at
+    `starting_line_number`, and the line previously at that position shifts down.
+    To insert at the very end instead, set starting_line_number = total_lines + 1
+    (or simply use append_to_document).
+
+    Args:
+        vault_name: Name of the vault.
+        doc_path: Relative path to the document.
+        starting_line_number: 1-indexed line where new_content begins (>= 1).
+        new_content: Markdown text to insert (may be multiple lines).
+
+    Returns the updated document info.
+    """
+    _sync_pre_read(vault_name)
+    if not doc_path.lower().endswith(".md"):
+        doc_path = doc_path.rstrip("/\\") + ".md"
+
+    target = _resolve_doc(vault_name, doc_path)
+    clean_path = doc_path.lstrip("/\\").replace("\\", "/")
+
+    existing = target.read_text(encoding="utf-8", errors="replace") if target.exists() else ""
+    lines = existing.splitlines(keepends=True)
+
+    new_lines = new_content.splitlines(keepends=True)
+    if not new_lines:
+        new_lines = ["\n"]
+
+    # Clamp insert position into [1, len(lines) + 1]
+    insert_at = max(1, min(starting_line_number, len(lines) + 1))
+    insert_idx = insert_at - 1
+
+    if lines and not lines[-1].endswith("\n"):
+        lines[-1] = lines[-1] + "\n"
+    if new_lines and not new_lines[-1].endswith("\n"):
+        new_lines[-1] = new_lines[-1] + "\n"
+
+    new_file_lines = lines[:insert_idx] + new_lines + lines[insert_idx:]
+    full = "".join(new_file_lines)
+
+    if not target.exists():
+        target.parent.mkdir(parents=True, exist_ok=True)
+
+    target.write_text(full, encoding="utf-8")
+    _sync_post_write(vault_name, clean_path, full)
+
+    return {
+        "vault": vault_name,
+        "path": clean_path,
+        "action": "inserted",
+        "inserted_at_line": insert_at,
         "size_bytes": target.stat().st_size,
     }
 
 
+@mcp.tool()
+def replace_document_lines(vault_name: str, doc_path: str, starting_line_number: int, ending_line_number: int, new_content: str) -> dict[str, Any]:
+    """Replace an inclusive range of lines [starting_line_number, ending_line_number]
+    with `new_content`. Pass new_content="" to delete the range outright.
+
+    1-indexed, inclusive on both ends. This is the safe in-place edit primitive:
+    no read-splice-overwrite of the whole file required.
+
+    Args:
+        vault_name: Name of the vault.
+        doc_path: Relative path to the document.
+        starting_line_number: 1-indexed first line of the range to replace (>= 1).
+        ending_line_number: 1-indexed last line of the range to replace (>= start).
+        new_content: Markdown text to substitute for the range (empty string deletes it).
+
+    Returns the updated document info.
+    """
+    _sync_pre_read(vault_name)
+    if not doc_path.lower().endswith(".md"):
+        doc_path = doc_path.rstrip("/\\") + ".md"
+
+    target = _resolve_doc(vault_name, doc_path)
+    if not target.exists():
+        return {"error": f"Document does not exist: {doc_path}", "vault": vault_name}
+
+    clean_path = doc_path.lstrip("/\\").replace("\\", "/")
+
+    existing = target.read_text(encoding="utf-8", errors="replace")
+    lines = existing.splitlines(keepends=True)
+    line_count = max(1, len(existing.splitlines()))
+
+    start = max(1, starting_line_number)
+    end = max(start, min(ending_line_number, line_count))
+    start_idx = start - 1
+    end_idx = end  # exclusive
+
+    new_lines = new_content.splitlines(keepends=True) if new_content else []
+    if new_lines and not new_lines[-1].endswith("\n"):
+        new_lines[-1] = new_lines[-1] + "\n"
+
+    new_file_lines = lines[:start_idx] + new_lines + lines[end_idx:]
+    full = "".join(new_file_lines)
+
+    target.write_text(full, encoding="utf-8")
+    _sync_post_write(vault_name, clean_path, full)
+
+    return {
+        "vault": vault_name,
+        "path": clean_path,
+        "action": "replaced_lines",
+        "replaced_line_start": start,
+        "replaced_line_end": end,
+        "size_bytes": target.stat().st_size,
+    }
+
+
+@mcp.tool()
+def append_to_document(vault_name: str, doc_path: str, content: str) -> dict[str, Any]:
+    """Append content to the end of a markdown document. Creates the file if it doesn't exist.
+
+    Args:
+        vault_name: Name of the vault.
+        doc_path: Relative path to the document.
+        content: Markdown content to append.
+
+    Returns the updated document info.
+    """
+    _sync_pre_read(vault_name)
+    if not doc_path.lower().endswith(".md"):
+        doc_path = doc_path.rstrip("/\\") + ".md"
+
+    target = _resolve_doc(vault_name, doc_path)
+    clean_path = doc_path.lstrip("/\\").replace("\\", "/")
+
+    if not target.exists():
+        target.parent.mkdir(parents=True, exist_ok=True)
+        target.write_text(content + "\n", encoding="utf-8")
+        action = "created"
+    else:
+        existing = target.read_text(encoding="utf-8", errors="replace")
+        separator = "\n" if existing.endswith("\n") else "\n\n"
+        full = existing + separator + content + "\n"
+        target.write_text(full, encoding="utf-8")
+        action = "appended"
+
+    # Sync — pass full content for embedding
+    full_content = target.read_text(encoding="utf-8", errors="replace")
+    _sync_post_write(vault_name, clean_path, full_content)
+
+    return {
+        "vault": vault_name,
+        "path": clean_path,
+        "action": action,
+        "size_bytes": target.stat().st_size,
+    }
+
+
+@mcp.tool()
+def delete_document(vault_name: str, doc_path: str) -> dict[str, Any]:
+    """Delete a document from a vault.
+
+    Args:
+        vault_name: Name of the vault.
+        doc_path: Relative path to the document.
+
+    Returns deletion confirmation.
+    """
+    _sync_pre_read(vault_name)
+    target = _resolve_doc(vault_name, doc_path)
+    if not target.exists():
+        return {"error": f"Document not found: {doc_path}", "vault": vault_name}
+
+    target.unlink()
+
+    clean_path = doc_path.lstrip("/\\").replace("\\", "/")
+    _sync_post_delete(vault_name, clean_path)
+
+    return {"vault": vault_name, "path": clean_path, "action": "deleted"}
+
+
 @mcp.tool()
 def create_vault_directory(vault_name: str, dir_path: str) -> dict[str, Any]:
     """FILESYSTEM TOOL (not memory) — Create a new directory in a vault on disk.
@@ -578,6 +980,7 @@ def move_document(vault_name: str, src_path: str, dest_path: str) -> dict[str, A
 
     Returns the move result with both old and new paths.
     """
+    _sync_pre_read(vault_name)
     src = _resolve_doc(vault_name, src_path)
     if not src.exists():
         return {"error": f"Source document does not exist: {src_path}", "vault": vault_name}
@@ -592,9 +995,21 @@ def move_document(vault_name: str, src_path: str, dest_path: str) -> dict[str, A
     src.rename(dest)
 
     vault = _vault_path(vault_name)
+    clean_src = src_path.lstrip("/\\").replace("\\", "/")
+    clean_dest = dest_path.lstrip("/\\").replace("\\", "/")
+
+    # Remove old ajson, embed new location
+    _delete_ajson_entry(vault, clean_src)
+    try:
+        content = dest.read_text(encoding="utf-8", errors="replace")
+        _write_ajson_entry(vault, clean_dest, content)
+    except Exception:
+        content = None
+    _git_commit_and_push(vault, f"[hermes] auto-sync: move {clean_src} -> {clean_dest}")
+
     return {
         "vault": vault_name,
-        "old_path": src_path.lstrip("/\\").replace("\\", "/"),
+        "old_path": clean_src,
         "new_path": str(dest.relative_to(vault)).replace("\\", "/"),
         "action": "moved",
     }
@@ -611,6 +1026,7 @@ def read_frontmatter(vault_name: str, doc_path: str, key: str | None = None) ->
 
     Returns the frontmatter dict or specific key value.
     """
+    _sync_pre_read(vault_name)
     target = _resolve_doc(vault_name, doc_path)
     if not target.exists():
         return {"error": f"Document not found: {doc_path}", "vault": vault_name}
@@ -637,6 +1053,7 @@ def write_frontmatter(vault_name: str, doc_path: str, key: str, value: Any = Non
 
     Returns the updated frontmatter state.
     """
+    _sync_pre_read(vault_name)
     target = _resolve_doc(vault_name, doc_path)
     if not target.exists():
         return {"error": f"Document not found: {doc_path}", "vault": vault_name}
@@ -651,73 +1068,26 @@ def write_frontmatter(vault_name: str, doc_path: str, key: str, value: Any = Non
         new_fm = {key: value}
         new_content = "---\n" + yaml.dump(new_fm, default_flow_style=False, allow_unicode=True).strip() + "\n---\n\n" + content
         target.write_text(new_content, encoding="utf-8")
-        return {"vault": vault_name, "path": doc_path, "key": key, "value": value, "action": "created"}
-
-    # Existing frontmatter
-    if value is None:
-        fm.pop(key, None)
-        action = "deleted"
     else:
-        fm[key] = value
-        action = "set"
+        # Existing frontmatter
+        if value is None:
+            fm.pop(key, None)
+            action = "deleted"
+        else:
+            fm[key] = value
+            action = "set"
 
-    new_fm_block = "---\n" + yaml.dump(fm, default_flow_style=False, allow_unicode=True).strip() + "\n---"
-    body = _body_after_frontmatter(content)
-    target.write_text(new_fm_block + "\n\n" + body, encoding="utf-8")
+        new_fm_block = "---\n" + yaml.dump(fm, default_flow_style=False, allow_unicode=True).strip() + "\n---"
+        body = _body_after_frontmatter(content)
+        new_content = new_fm_block + "\n\n" + body
+        target.write_text(new_content, encoding="utf-8")
 
-    return {"vault": vault_name, "path": doc_path, "key": key, "value": value, "action": action}
+    clean_path = doc_path.lstrip("/\\").replace("\\", "/")
+    # Re-read the full content for embedding
+    full_content = target.read_text(encoding="utf-8", errors="replace")
+    _sync_post_write(vault_name, clean_path, full_content)
 
-
-@mcp.tool()
-def append_to_document(vault_name: str, doc_path: str, content: str) -> dict[str, Any]:
-    """Append content to the end of a markdown document. Creates the file if it doesn't exist.
-
-    Args:
-        vault_name: Name of the vault.
-        doc_path: Relative path to the document.
-        content: Markdown content to append.
-
-    Returns the updated document info.
-    """
-    if not doc_path.lower().endswith(".md"):
-        doc_path = doc_path.rstrip("/\\") + ".md"
-
-    target = _resolve_doc(vault_name, doc_path)
-
-    if not target.exists():
-        target.parent.mkdir(parents=True, exist_ok=True)
-        target.write_text(content + "\n", encoding="utf-8")
-        action = "created"
-    else:
-        existing = target.read_text(encoding="utf-8", errors="replace")
-        separator = "\n" if existing.endswith("\n") else "\n\n"
-        target.write_text(existing + separator + content + "\n", encoding="utf-8")
-        action = "appended"
-
-    return {
-        "vault": vault_name,
-        "path": doc_path.lstrip("/\\").replace("\\", "/"),
-        "action": action,
-        "size_bytes": target.stat().st_size,
-    }
-
-
-@mcp.tool()
-def delete_document(vault_name: str, doc_path: str) -> dict[str, Any]:
-    """Delete a document from a vault.
-
-    Args:
-        vault_name: Name of the vault.
-        doc_path: Relative path to the document.
-
-    Returns deletion confirmation.
-    """
-    target = _resolve_doc(vault_name, doc_path)
-    if not target.exists():
-        return {"error": f"Document not found: {doc_path}", "vault": vault_name}
-
-    target.unlink()
-    return {"vault": vault_name, "path": doc_path.lstrip("/\\").replace("\\", "/"), "action": "deleted"}
+    return {"vault": vault_name, "path": clean_path, "key": key, "value": value, "action": action}
 
 
 def _parse_frontmatter(content: str) -> dict[str, Any] | None:
@@ -763,17 +1133,25 @@ def main():
         default="0.0.0.0",
         help="Bind host (default: 0.0.0.0 for LAN access)",
     )
+    parser.add_argument(
+        "--transport",
+        choices=["streamable-http", "stdio"],
+        default="streamable-http",
+        help="Transport mode: streamable-http (network) or stdio (subprocess) (default: streamable-http)",
+    )
     args = parser.parse_args()
 
     global VAULTS_ROOT
     VAULTS_ROOT = resolve_vaults_root(args.vaults_root)
 
-    print(f"Obsidian MCP Server")
-    print(f"  Vaults root: {VAULTS_ROOT}")
-    print(f"  Listening:   http://{args.host}:{args.port}/mcp")
-    print(f"  Vaults found: {len(get_vaults()['vaults'])}")
-
-    mcp.run(transport="streamable-http", host=args.host, port=args.port, path="/mcp")
+    if args.transport == "stdio":
+        mcp.run(transport="stdio")
+    else:
+        print(f"Obsidian MCP Server")
+        print(f"  Vaults root: {VAULTS_ROOT}")
+        print(f"  Listening:   http://{args.host}:{args.port}/mcp")
+        print(f"  Vaults found: {len(get_vaults()['vaults'])}")
+        mcp.run(transport="streamable-http", host=args.host, port=args.port, path="/mcp")
 
 
 if __name__ == "__main__":