diff --git a/CHANGELOG.md b/CHANGELOG.md
index e38204d..cb7ba51 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -19,6 +19,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Vault path resolution: `home_dir` IPC command (`dirs`) + `resolveHomePath` in core — `~/` and relative vault paths now resolve to absolute paths anywhere on disk
 - `trachyte doctor` dev-tools: `doctor` IPC command (vault validity + missing dirs/files + `schema_version` value), core aggregator (`buildDoctorReport` / `settingsValidity` reusing `isSettings`), and a `DoctorPanel` opened via the sidebar "Run doctor" button or `Ctrl+Shift+D`
 
+- `trachyte-db` SQLite bootstrap: `Database` wrapper (open → pragmas → migrate) with `PRAGMA journal_mode=WAL`/`synchronous=NORMAL`/`foreign_keys=ON`; schema v1 (`files`/`headings`/`tags`/`backlinks` with `ON DELETE CASCADE`); FTS5 mirror table `content_fts` (porter tokenizer) + `search`; BLAKE3 `hash_content`; versioned migration runner (`PRAGMA user_version`, one tx per migration)
+
 ### Changed
 
 - CI Hardening for `ci.yml` now checks inside app/desktop to confirm build ablility
diff --git a/Cargo.lock b/Cargo.lock
index fcbc345..2b58768 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -3676,6 +3676,7 @@ dependencies = [
  "rusqlite",
  "serde",
  "serde_json",
+ "tempfile",
  "thiserror 2.0.18",
 ]
 
diff --git a/crates/trachyte-db/Cargo.toml b/crates/trachyte-db/Cargo.toml
index 4640b30..0667d3d 100644
--- a/crates/trachyte-db/Cargo.toml
+++ b/crates/trachyte-db/Cargo.toml
@@ -10,3 +10,6 @@ serde_json = { workspace = true }
 thiserror = { workspace = true }
 rusqlite = { workspace = true }
 blake3 = { workspace = true }
+
+[dev-dependencies]
+tempfile = { workspace = true }
diff --git a/crates/trachyte-db/src/error.rs b/crates/trachyte-db/src/error.rs
new file mode 100644
index 0000000..36c41ee
--- /dev/null
+++ b/crates/trachyte-db/src/error.rs
@@ -0,0 +1,11 @@
+//! Database error type for the SQLite index crate.
+
+use thiserror::Error;
+
+/// Errors that can occur during database operations.
+#[derive(Debug, Error)]
+pub enum DbError {
+    /// Wrapped SQLite error.
+    #[error("sqlite: {0}")]
+    Sql(#[from] rusqlite::Error),
+}
diff --git a/crates/trachyte-db/src/fts.rs b/crates/trachyte-db/src/fts.rs
index 9947f48..501170b 100644
--- a/crates/trachyte-db/src/fts.rs
+++ b/crates/trachyte-db/src/fts.rs
@@ -1 +1,67 @@
 //! FTS5 virtual table operations.
+
+use rusqlite::{params, Connection};
+
+use crate::DbError;
+
+/// FTS5 virtual table mirroring file contents for full-text search.
+pub const FTS5_SCHEMA: &str = "
+CREATE VIRTUAL TABLE content_fts USING fts5(
+  path UNINDEXED,
+  content,
+  tokenize = 'porter'
+);
+";
+
+/// Insert the FTS mirror row for a file.
+pub fn insert_content(conn: &Connection, path: &str, content: &str) -> Result<(), DbError> {
+    conn.execute(
+        "INSERT INTO content_fts(path, content) VALUES (?1, ?2)",
+        params![path, content],
+    )?;
+    Ok(())
+}
+
+/// Full-text search over file contents; returns matching paths.
+pub fn search(conn: &Connection, query: &str) -> Result<Vec<String>, DbError> {
+    let mut stmt =
+        conn.prepare("SELECT path FROM content_fts WHERE content_fts MATCH ?1 ORDER BY rank")?;
+    let rows = stmt.query_map(params![query], |row| row.get(0))?;
+    let mut paths = Vec::new();
+    for row in rows {
+        paths.push(row?);
+    }
+    Ok(paths)
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+    use tempfile::tempdir;
+
+    fn setup() -> (tempfile::TempDir, rusqlite::Connection) {
+        let dir = tempdir().unwrap();
+        let conn = rusqlite::Connection::open(dir.path().join("test.db")).unwrap();
+        conn.execute_batch(FTS5_SCHEMA).unwrap();
+        (dir, conn)
+    }
+
+    #[test]
+    fn search_returns_matching_paths() {
+        let (_dir, conn) = setup();
+        insert_content(
+            &conn,
+            "Notes/Java.md",
+            "Object-oriented programming language",
+        )
+        .unwrap();
+        insert_content(&conn, "Notes/Rust.md", "Systems programming language").unwrap();
+
+        let hits = search(&conn, "programming").unwrap();
+        assert!(hits.contains(&"Notes/Java.md".to_string()));
+        assert!(hits.contains(&"Notes/Rust.md".to_string()));
+
+        let rust = search(&conn, "systems").unwrap();
+        assert_eq!(rust, vec!["Notes/Rust.md".to_string()]);
+    }
+}
diff --git a/crates/trachyte-db/src/hash.rs b/crates/trachyte-db/src/hash.rs
index 09db059..e5a000d 100644
--- a/crates/trachyte-db/src/hash.rs
+++ b/crates/trachyte-db/src/hash.rs
@@ -1 +1,25 @@
 //! BLAKE3 content hashing.
+
+/// Hash content bytes with BLAKE3 and return the hex digest.
+pub fn hash_content(bytes: impl AsRef<[u8]>) -> String {
+    blake3::hash(bytes.as_ref()).to_hex().to_string()
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    #[test]
+    fn hash_content_known_value() {
+        assert_eq!(
+            hash_content(b"hello world"),
+            "d74981efa70a0c880b8d8c1985d075dbcbf679b99a5f9914e5aaf96b831a9e24"
+        );
+    }
+
+    #[test]
+    fn hash_is_stable_and_sensitive() {
+        assert_eq!(hash_content(b"abc"), hash_content(b"abc"));
+        assert_ne!(hash_content(b"abc"), hash_content(b"abd"));
+    }
+}
diff --git a/crates/trachyte-db/src/lib.rs b/crates/trachyte-db/src/lib.rs
index 313059e..cc45adb 100644
--- a/crates/trachyte-db/src/lib.rs
+++ b/crates/trachyte-db/src/lib.rs
@@ -1,9 +1,108 @@
-#![deny(missing_docs)]
-
 //! SQLite index with FTS5 search (WAL mode).
 
+use std::path::Path;
+
+use rusqlite::Connection;
+
+pub mod error;
 pub mod fts;
 pub mod hash;
 pub mod migrations;
 pub mod pragmas;
 pub mod schema;
+
+pub use error::DbError;
+
+/// A SQLite index database with WAL + FTS5 configured.
+pub struct Database {
+    conn: Connection,
+}
+
+impl Database {
+    /// Open (or create) an index database at `path`, applying pragmas and
+    /// running pending migrations.
+    ///
+    /// The parent directory must already exist (the vault's `.trachyte/`
+    /// guarantees this); it is not created.
+    pub fn open(path: impl AsRef<Path>) -> Result<Database, DbError> {
+        let mut conn = Connection::open(path)?;
+        pragmas::apply_pragmas(&conn)?;
+        migrations::migrate(&mut conn)?;
+        Ok(Database { conn })
+    }
+
+    /// Insert a file and its content into the index, returning its row id.
+    ///
+    /// `hash` should be the BLAKE3 hex digest of `content`
+    /// (see [`hash::hash_content`]); the caller computes `size`.
+    pub fn insert_file(
+        &self,
+        path: &str,
+        content: &str,
+        mtime: i64,
+        size: i64,
+        hash: &str,
+    ) -> Result<i64, DbError> {
+        self.conn.execute(
+            "INSERT INTO files (path, mtime, size, hash) VALUES (?1, ?2, ?3, ?4)",
+            rusqlite::params![path, mtime, size, hash],
+        )?;
+        let id = self.conn.last_insert_rowid();
+        fts::insert_content(&self.conn, path, content)?;
+        Ok(id)
+    }
+
+    /// Full-text search over file contents; returns matching paths.
+    pub fn search(&self, query: &str) -> Result<Vec<String>, DbError> {
+        fts::search(&self.conn, query)
+    }
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+    use tempfile::tempdir;
+
+    fn open_db() -> (tempfile::TempDir, Database) {
+        let dir = tempdir().unwrap();
+        let db = Database::open(dir.path().join("index.db")).unwrap();
+        (dir, db)
+    }
+
+    #[test]
+    fn insert_and_search_roundtrip() {
+        let (_dir, db) = open_db();
+        let content = "# Hello\n\nThis is my note about databases.";
+        db.insert_file(
+            "Notes/Hello.md",
+            content,
+            1_700_000_000,
+            content.len() as i64,
+            &hash::hash_content(content),
+        )
+        .unwrap();
+
+        let hits = db.search("databases").unwrap();
+        assert_eq!(hits, vec!["Notes/Hello.md".to_string()]);
+    }
+
+    #[test]
+    fn search_misses_for_unknown_term() {
+        let (_dir, db) = open_db();
+        db.insert_file("Notes/A.md", "alpha beta", 0, 10, "deadbeef")
+            .unwrap();
+
+        assert!(db.search("omega").unwrap().is_empty());
+    }
+
+    #[test]
+    fn wal_file_present_after_first_write() {
+        let dir = tempdir().unwrap();
+        let db = Database::open(dir.path().join("index.db")).unwrap();
+
+        db.insert_file("Notes/A.md", "wal test", 0, 8, "deadbeef")
+            .unwrap();
+
+        assert!(dir.path().join("index.db-wal").exists());
+    }
+}
diff --git a/crates/trachyte-db/src/migrations.rs b/crates/trachyte-db/src/migrations.rs
index 29b68ad..38424a6 100644
--- a/crates/trachyte-db/src/migrations.rs
+++ b/crates/trachyte-db/src/migrations.rs
@@ -1 +1,74 @@
 //! Migration runner.
+
+use rusqlite::Connection;
+
+use crate::fts;
+use crate::schema;
+use crate::DbError;
+
+/// Run any unapplied migrations, each inside its own transaction
+/// Version 1 creates the relational tables (`schema::SCHEMA_V1`) and the
+/// FTS5 mirror (`fts::FTS5_SCHEMA`) together, bumping `user_version` to 1
+pub fn migrate(conn: &mut Connection) -> Result<(), DbError> {
+    let version: i64 = conn.query_row("PRAGMA user_version", [], |row| row.get(0))?;
+    if version < 1 {
+        let tx = conn.transaction()?;
+        tx.execute_batch(schema::SCHEMA_V1)?;
+        tx.execute_batch(fts::FTS5_SCHEMA)?;
+        tx.pragma_update(None, "user_version", 1)?;
+        tx.commit()?;
+    }
+    Ok(())
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+    use tempfile::tempdir;
+
+    #[test]
+    fn migrate_creates_schema_and_sets_version() {
+        let dir = tempdir().unwrap();
+        let mut conn = rusqlite::Connection::open(dir.path().join("test.db")).unwrap();
+
+        migrate(&mut conn).unwrap();
+        let version: i64 = conn
+            .query_row("PRAGMA user_version", [], |row| row.get(0))
+            .unwrap();
+        assert_eq!(version, 1);
+
+        let objects: Vec<String> = conn
+            .prepare("SELECT name FROM sqlite_master WHERE type IN ('table', 'index')")
+            .unwrap()
+            .query_map([], |row| row.get(0))
+            .unwrap()
+            .collect::<Result<Vec<String>, _>>()
+            .unwrap();
+
+        for expected in [
+            "files",
+            "headings",
+            "tags",
+            "backlinks",
+            "content_fts",
+            "idx_tags_tag",
+            "idx_backlinks_target",
+        ] {
+            assert!(objects.iter().any(|o| o == expected), "missing {expected}");
+        }
+    }
+
+    #[test]
+    fn migrate_is_idempotent() {
+        let dir = tempdir().unwrap();
+        let mut conn = rusqlite::Connection::open(dir.path().join("test.db")).unwrap();
+
+        migrate(&mut conn).unwrap();
+        migrate(&mut conn).unwrap();
+
+        let version: i64 = conn
+            .query_row("PRAGMA user_version", [], |row| row.get(0))
+            .unwrap();
+        assert_eq!(version, 1);
+    }
+}
diff --git a/crates/trachyte-db/src/pragmas.rs b/crates/trachyte-db/src/pragmas.rs
index 76963be..da53b70 100644
--- a/crates/trachyte-db/src/pragmas.rs
+++ b/crates/trachyte-db/src/pragmas.rs
@@ -1 +1,43 @@
 //! WAL + foreign_keys + synchronous pragmas.
+
+use rusqlite::Connection;
+
+use crate::DbError;
+
+/// Apply the connection-level pragmas required by the vault contract:
+/// WAL journaling, `synchronous=NORMAL`, and foreign key enforcement
+/// Must run before any transaction (WAL mode cannot be enabled inside one)
+pub fn apply_pragmas(conn: &Connection) -> Result<(), DbError> {
+    conn.pragma_update(None, "journal_mode", "wal")?;
+    conn.pragma_update(None, "synchronous", "NORMAL")?;
+    conn.pragma_update(None, "foreign_keys", "ON")?;
+    Ok(())
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+    use tempfile::tempdir;
+
+    #[test]
+    fn open_applies_pragmas() {
+        let dir = tempdir().unwrap();
+        let conn = rusqlite::Connection::open(dir.path().join("test.db")).unwrap();
+
+        apply_pragmas(&conn).unwrap();
+
+        let journal_mode: String = conn
+            .pragma_query_value(None, "journal_mode", |row| row.get(0))
+            .unwrap();
+        let synchronous: i64 = conn
+            .pragma_query_value(None, "synchronous", |row| row.get(0))
+            .unwrap();
+        let foreign_keys: i64 = conn
+            .pragma_query_value(None, "foreign_keys", |row| row.get(0))
+            .unwrap();
+
+        assert_eq!(journal_mode, "wal");
+        assert_eq!(synchronous, 1);
+        assert_eq!(foreign_keys, 1);
+    }
+}
diff --git a/crates/trachyte-db/src/schema.rs b/crates/trachyte-db/src/schema.rs
index e6296ea..14febf7 100644
--- a/crates/trachyte-db/src/schema.rs
+++ b/crates/trachyte-db/src/schema.rs
@@ -1 +1,37 @@
 //! Schema definitions.
+
+/// Schema version 1 for the project
+/// The FTS5 mirror lives in [`super::fts::FTS5_SCHEMA`]; migrations apply
+/// both together. `files` is the parent of every other table;
+/// deleting a file cascades to its headings, tags, and backlinks
+pub const SCHEMA_V1: &str = "
+CREATE TABLE files (
+  id INTEGER PRIMARY KEY,
+  path TEXT NOT NULL UNIQUE,
+  mtime INTEGER NOT NULL,
+  size INTEGER NOT NULL,
+  hash TEXT NOT NULL,
+  schema_version INTEGER NOT NULL DEFAULT 1
+);
+
+CREATE TABLE headings (
+  file_id INTEGER NOT NULL REFERENCES files(id) ON DELETE CASCADE,
+  level INTEGER NOT NULL,
+  text TEXT NOT NULL,
+  position INTEGER NOT NULL
+);
+
+CREATE TABLE tags (
+  file_id INTEGER NOT NULL REFERENCES files(id) ON DELETE CASCADE,
+  tag TEXT NOT NULL
+);
+
+CREATE TABLE backlinks (
+  target_file_id INTEGER NOT NULL REFERENCES files(id) ON DELETE CASCADE,
+  source_file_id INTEGER NOT NULL REFERENCES files(id) ON DELETE CASCADE,
+  position_char INTEGER NOT NULL
+);
+
+CREATE INDEX idx_tags_tag ON tags(tag);
+CREATE INDEX idx_backlinks_target ON backlinks(target_file_id);
+";