feat(config): restore path aliases with TS 6.x-compatible subpath imports

crates/codegraph-core/src/native_db.rs

@@ -8,7 +8,7 @@
 //! Any changes there MUST be reflected here (and vice-versa).
 
 use napi_derive::napi;
-use rusqlite::{params, Connection, OpenFlags};
+use rusqlite::{params, types::ValueRef, Connection, OpenFlags};
 use send_wrapper::SendWrapper;
 
 use crate::ast_db::{self, FileAstBatch};
@@ -549,6 +549,104 @@ impl NativeDatabase {
         Ok(())
     }
 
+    // ── Phase 6.16: Generic query execution & version validation ────────
+
+    /// Execute a parameterized query and return all rows as JSON objects.
+    /// Each row is a `{ column_name: value, ... }` object.
+    /// Params are positional (`?1, ?2, ...`) and accept string, number, or null.
+    ///
+    /// **Note**: Designed for SELECT statements. Passing DML/DDL will not error
+    /// at the Rust layer but is not an intended use — all current callers pass
+    /// SELECT-only SQL generated by `NodeQuery.build()`.
+    #[napi]
+    pub fn query_all(
+        &self,
+        sql: String,
+        params: Vec<serde_json::Value>,
+    ) -> napi::Result<Vec<serde_json::Value>> {
+        let conn = self.conn()?;
+        let rusqlite_params = json_to_rusqlite_params(&params)?;
+        let param_refs: Vec<&dyn rusqlite::types::ToSql> =
+            rusqlite_params.iter().map(|v| v as &dyn rusqlite::types::ToSql).collect();
+
+        let mut stmt = conn
+            .prepare(&sql)
+            .map_err(|e| napi::Error::from_reason(format!("queryAll prepare failed: {e}")))?;
+
+        let col_count = stmt.column_count();
+        let col_names: Vec<String> = (0..col_count)
+            .map(|i| stmt.column_name(i).unwrap_or("?").to_owned())
+            .collect();
+
+        let rows = stmt
+            .query_map(param_refs.as_slice(), |row| {
+                Ok(row_to_json(row, col_count, &col_names))
+            })
+            .map_err(|e| napi::Error::from_reason(format!("queryAll query failed: {e}")))?;
+
+        let mut result = Vec::new();
+        for row in rows {
+            let val =
+                row.map_err(|e| napi::Error::from_reason(format!("queryAll row failed: {e}")))?;
+            result.push(val);
+        }
+        Ok(result)
+    }
+
+    /// Execute a parameterized query and return the first row, or null.
+    /// See `query_all` for parameter and contract details.
+    #[napi]
+    pub fn query_get(
+        &self,
+        sql: String,
+        params: Vec<serde_json::Value>,
+    ) -> napi::Result<Option<serde_json::Value>> {
+        let conn = self.conn()?;
+        let rusqlite_params = json_to_rusqlite_params(&params)?;
+        let param_refs: Vec<&dyn rusqlite::types::ToSql> =
+            rusqlite_params.iter().map(|v| v as &dyn rusqlite::types::ToSql).collect();
+
+        let mut stmt = conn
+            .prepare(&sql)
+            .map_err(|e| napi::Error::from_reason(format!("queryGet prepare failed: {e}")))?;
+
+        let col_count = stmt.column_count();
+        let col_names: Vec<String> = (0..col_count)
+            .map(|i| stmt.column_name(i).unwrap_or("?").to_owned())
+            .collect();
+
+        let mut query_rows = stmt
+            .query(param_refs.as_slice())
+            .map_err(|e| napi::Error::from_reason(format!("queryGet query failed: {e}")))?;
+
+        match query_rows.next() {
+            Ok(Some(row)) => Ok(Some(row_to_json(row, col_count, &col_names))),
+            Ok(None) => Ok(None),
+            Err(e) => Err(napi::Error::from_reason(format!(
+                "queryGet row failed: {e}"
+            ))),
+        }
+    }
+
+    /// Validate that the DB's codegraph_version matches the expected version.
+    /// Returns `true` if versions match or no version is stored.
+    /// Prints a warning to stderr on mismatch.
+    #[napi]
+    pub fn validate_schema_version(&self, expected_version: String) -> napi::Result<bool> {
+        let stored = self.get_build_meta("codegraph_version".to_string())?;
+        match stored {
+            None => Ok(true),
+            Some(ref v) if v == &expected_version => Ok(true),
+            Some(v) => {
+                eprintln!(
+                    "[codegraph] DB was built with v{v}, running v{expected_version}. \
+                     Consider: codegraph build --no-incremental"
+                );
+                Ok(false)
+            }
+        }
+    }
+
     // ── Phase 6.15: Build pipeline write operations ─────────────────────
 
     /// Bulk-insert nodes, children, containment edges, exports, and file hashes.
@@ -698,3 +796,62 @@ fn has_column(conn: &Connection, table: &str, column: &str) -> bool {
         Err(_) => false,
     }
 }
+
+/// Convert a JSON param array to rusqlite-compatible values.
+fn json_to_rusqlite_params(
+    params: &[serde_json::Value],
+) -> napi::Result<Vec<rusqlite::types::Value>> {
+    params
+        .iter()
+        .enumerate()
+        .map(|(i, v)| match v {
+            serde_json::Value::Null => Ok(rusqlite::types::Value::Null),
+            serde_json::Value::Number(n) => {
+                if let Some(int) = n.as_i64() {
+                    Ok(rusqlite::types::Value::Integer(int))
+                } else if let Some(float) = n.as_f64() {
+                    Ok(rusqlite::types::Value::Real(float))
+                } else {
+                    Err(napi::Error::from_reason(format!(
+                        "param[{i}]: unsupported number {n}"
+                    )))
+                }
+            }
+            serde_json::Value::String(s) => Ok(rusqlite::types::Value::Text(s.clone())),
+            other => Err(napi::Error::from_reason(format!(
+                "param[{i}]: unsupported type {}",
+                other
+            ))),
+        })
+        .collect()
+}
+
+/// Convert a rusqlite row to a serde_json::Value object.
+///
+/// **Contract**: Only Integer, Real, Text, and Null column types are supported.
+/// BLOB columns are mapped to `null` because the current codegraph schema has no
+/// BLOB columns and the generic query path is not designed for binary data.
+/// Cell-level read errors are also mapped to `null` to avoid partial-row failures.
+fn row_to_json(
+    row: &rusqlite::Row<'_>,
+    col_count: usize,
+    col_names: &[String],
+) -> serde_json::Value {
+    let mut map = serde_json::Map::with_capacity(col_count);
+    for i in 0..col_count {
+        let val = match row.get_ref(i) {
+            Ok(ValueRef::Integer(n)) => serde_json::json!(n),
+            Ok(ValueRef::Real(f)) => serde_json::json!(f),
+            Ok(ValueRef::Text(s)) => {
+                serde_json::Value::String(String::from_utf8_lossy(s).into_owned())
+            }
+            Ok(ValueRef::Null) => serde_json::Value::Null,
+            // BLOB: no codegraph schema columns use BLOB; map to null (see contract above)
+            Ok(ValueRef::Blob(_)) => serde_json::Value::Null,
+            // Cell read error: map to null to avoid partial-row failures
+            Err(_) => serde_json::Value::Null,
+        };
+        map.insert(col_names[i].clone(), val);
+    }
+    serde_json::Value::Object(map)
+}

docs/migration/db-prepare-audit.md

@@ -0,0 +1,127 @@
+# `db.prepare()` Migration Audit
+
+> **Phase 6.16** — Audit of all direct `better-sqlite3` `.prepare()` calls.
+> Goal: every call routes through either `Repository` or `NativeDatabase` methods.
+
+## Summary
+
+| Tier | Layer | Files | Calls | Status |
+|------|-------|-------|-------|--------|
+| 0 | DB infrastructure | 4 | 7 | Done (repository + migrations) |
+| 0 | Starter migrations | 2 | 3 | Done (6.16 PR) |
+| 1 | Build pipeline | 7 | 52 | Next — ctx.nativeDb available |
+| 2 | Domain analysis | 8 | 29 | Requires NativeDatabase in read path |
+| 3 | Features | 14 | 94 | Requires NativeDatabase in read path |
+| 3 | Shared utilities | 3 | 9 | Requires NativeDatabase in read path |
+| — | **Total** | **43** | **194** | — |
+
+## Tier 0 — Already Abstracted
+
+These are either inside the Repository pattern or in schema migration code.
+
+| File | Calls | Notes |
+|------|-------|-------|
+| `db/repository/build-stmts.ts` | 3 | Repository layer |
+| `db/repository/cfg.ts` | 1 | Repository layer |
+| `db/migrations.ts` | 3 | Schema DDL — keep as-is |
+
+## Tier 0 — Starter Migrations (6.16 PR)
+
+Converted to `nativeDb` dispatch in the 6.16 PR:
+
+| File | Calls | What |
+|------|-------|------|
+| `domain/graph/builder/stages/detect-changes.ts` | 2 | file_hashes probe + full read |
+| `domain/graph/builder/stages/build-structure.ts` | 1 | file node count |
+
+## Tier 1 — Build Pipeline (ctx.nativeDb available)
+
+These run during the build pipeline where `ctx.nativeDb` is already open.
+Migrate using the same `ctx.nativeDb ? nativeDb.queryAll/queryGet(...) : db.prepare(...)` pattern.
+
+| File | Calls | What |
+|------|-------|------|
+| `domain/graph/builder/stages/build-structure.ts` | 10 | dir metrics, role UPDATEs, line counts |
+| `domain/graph/builder/stages/detect-changes.ts` | 7 | journal queries, mtime checks, CFG count |
+| `domain/graph/builder/incremental.ts` | 6 | incremental rebuild queries |
+| `domain/graph/builder/stages/build-edges.ts` | 5 | edge dedup, containment edges |
+| `domain/graph/builder/stages/finalize.ts` | 5 | build metadata, embedding count |
+| `domain/graph/builder/stages/resolve-imports.ts` | 4 | import resolution lookups |
+| `domain/graph/builder/stages/insert-nodes.ts` | 3 | node insertion (JS fallback path) |
+| `domain/graph/builder/stages/collect-files.ts` | 2 | file collection queries |
+| `domain/graph/builder/helpers.ts` | 2 | utility queries |
+| `domain/graph/watcher.ts` | 9 | watch mode incremental |
+
+## Tier 2 — Domain Analysis (query-time, read-only)
+
+These run in the query pipeline which currently uses `openReadonlyOrFail()` (better-sqlite3 only).
+Migrating these requires adding NativeDatabase to the read path.
+
+| File | Calls | What |
+|------|-------|------|
+| `domain/analysis/module-map.ts` | 20 | Module map queries (heaviest file) |
+| `domain/analysis/symbol-lookup.ts` | 2 | Symbol search |
+| `domain/analysis/dependencies.ts` | 2 | Dependency queries |
+| `domain/analysis/diff-impact.ts` | 1 | Diff impact analysis |
+| `domain/analysis/exports.ts` | 1 | Export analysis |
+| `domain/analysis/fn-impact.ts` | 1 | Function impact |
+| `domain/analysis/roles.ts` | 1 | Role queries |
+| `domain/search/generator.ts` | 4 | Embedding generation |
+| `domain/search/stores/fts5.ts` | 1 | FTS5 search |
+| `domain/search/search/keyword.ts` | 1 | Keyword search |
+| `domain/search/search/prepare.ts` | 1 | Search preparation |
+
+## Tier 3 — Features Layer (query-time, read-only)
+
+Same dependency as Tier 2 — requires NativeDatabase in the read path.
+
+| File | Calls | What |
+|------|-------|------|
+| `features/structure.ts` | 21 | Structure analysis (heaviest) |
+| `features/export.ts` | 13 | Graph export |
+| `features/dataflow.ts` | 10 | Dataflow analysis |
+| `features/structure-query.ts` | 9 | Structure queries |
+| `features/audit.ts` | 7 | Audit command |
+| `features/cochange.ts` | 6 | Co-change analysis |
+| `features/branch-compare.ts` | 4 | Branch comparison |
+| `features/check.ts` | 3 | CI check predicates |
+| `features/owners.ts` | 3 | CODEOWNERS integration |
+| `features/cfg.ts` | 2 | Control flow graph |
+| `features/ast.ts` | 2 | AST queries |
+| `features/manifesto.ts` | 2 | Rule engine |
+| `features/sequence.ts` | 2 | Sequence diagrams |
+| `features/complexity.ts` | 1 | Complexity metrics |
+| `features/boundaries.ts` | 1 | Architecture boundaries |
+| `features/shared/find-nodes.ts` | 1 | Shared node finder |
+
+## Tier 3 — Shared Utilities
+
+| File | Calls | What |
+|------|-------|------|
+| `shared/generators.ts` | 4 | Generator utilities |
+| `shared/hierarchy.ts` | 4 | Hierarchy traversal |
+| `shared/normalize.ts` | 1 | Normalization helpers |
+
+## Migration Recipe
+
+### For Tier 1 (build pipeline):
+```typescript
+// Before:
+const row = db.prepare('SELECT ...').get(...args);
+
+// After:
+const sql = 'SELECT ...';
+const row = ctx.nativeDb
+  ? ctx.nativeDb.queryGet(sql, [...args])
+  : db.prepare(sql).get(...args);
+```
+
+### For Tiers 2-3 (query pipeline):
+Requires adding a `nativeDb` parameter to query-path functions, or opening
+a NativeDatabase in `openReadonlyOrFail()`. This is phase 6.17+ work.
+
+## Decision Log
+
+- **`iterate()` stays on better-sqlite3**: rusqlite can't stream across FFI. Only used by `iterateFunctionNodes` — bounded row counts.
+- **Migrations stay as-is**: Schema DDL runs once, no performance concern.
+- **Features/analysis layers blocked on read-path NativeDatabase**: These only have a better-sqlite3 handle via `openReadonlyOrFail()`. Adding NativeDatabase to the read path is a phase 6.17 prerequisite.

docs/roadmap/ROADMAP.md

@@ -1322,16 +1322,17 @@ Structure building is unchanged — at 22ms it's already fast.
 
 ### 6.16 -- Dynamic SQL & Edge Cases
 
-**Not started.** Handle the remaining non-trivial DB patterns that don't map cleanly to fixed Repository methods.
+**Done.** Generic parameterized query execution on NativeDatabase, connection lifecycle helpers, version validation, and `db.prepare()` audit.
 
-**Plan:**
-- **`NodeQuery` builder edge cases:** Ensure the Rust-side replica handles all filter combinations, JOIN paths, ORDER BY variations, and LIMIT/OFFSET correctly — fuzz-test with random filter combinations against the JS builder
-- **`openReadonlyOrFail` version-check logic:** Port the schema-version validation that runs on read-only DB opens
-- **Advisory lock mechanism:** Keep in JS (filesystem-based, not SQLite) — ensure `NativeDatabase.close()` integrates with the existing lock lifecycle
-- **`closeDbDeferred` / WAL checkpoint deferral:** Keep deferred-close logic in JS, call `NativeDatabase.close()` when ready
-- **Raw `db.prepare()` stragglers:** Audit all 383 callers of `.prepare()` and ensure every one routes through either `Repository` or `NativeDatabase` methods — no direct better-sqlite3 usage on the native path
+**Delivered:**
+- **`NativeDatabase.queryAll` / `queryGet`:** Generic parameterized SELECT execution via rusqlite, returning rows as JSON objects. Uses `serde_json::Value` for dynamic column support
+- **`NodeQuery` native dispatch:** `all()` and `get()` accept optional `nativeDb` parameter for rusqlite execution. Combinatorial parity test suite covers all filter/JOIN/ORDER BY combinations
+- **`NativeDatabase.validateSchemaVersion`:** Schema version check for future read-path callers
+- **`closeDbPair` / `closeDbPairDeferred`:** Unified connection lifecycle helpers — close NativeDatabase first (fast), then better-sqlite3 (WAL checkpoint). Replaces manual close sequences in `finalize.ts` and `pipeline.ts`
+- **Starter straggler migrations:** 3 build-pipeline reads in `detect-changes.ts` and `build-structure.ts` dispatch through `nativeDb` when available
+- **`db.prepare()` audit:** 194 calls across 43 files documented in `docs/migration/db-prepare-audit.md` with tiered migration path (Tier 0 done, Tier 1 build pipeline next, Tiers 2-3 blocked on read-path NativeDatabase)
 
-**Affected files:** `crates/codegraph-core/src/native_db.rs`, `src/db/connection.ts`, `src/db/query-builder.ts`, `src/db/repository/sqlite-repository.ts`
+**Affected files:** `crates/codegraph-core/src/native_db.rs`, `src/db/connection.ts`, `src/db/query-builder.ts`, `src/db/repository/nodes.ts`, `src/types.ts`, `src/domain/graph/builder/stages/finalize.ts`, `src/domain/graph/builder/pipeline.ts`, `src/domain/graph/builder/stages/detect-changes.ts`, `src/domain/graph/builder/stages/build-structure.ts`
 
 ### 6.17 -- Cleanup & better-sqlite3 Isolation
 

package.json

@@ -4,6 +4,20 @@
   "description": "Local code graph CLI — parse codebases with tree-sitter, build dependency graphs, query them",
   "type": "module",
   "main": "dist/index.js",
+  "imports": {
+    "#shared/*": { "@codegraph/source": "./src/shared/*", "default": "./dist/shared/*" },
+    "#infrastructure/*": { "@codegraph/source": "./src/infrastructure/*", "default": "./dist/infrastructure/*" },
+    "#db/*": { "@codegraph/source": "./src/db/*", "default": "./dist/db/*" },
+    "#domain/*": { "@codegraph/source": "./src/domain/*", "default": "./dist/domain/*" },
+    "#features/*": { "@codegraph/source": "./src/features/*", "default": "./dist/features/*" },
+    "#presentation/*": { "@codegraph/source": "./src/presentation/*", "default": "./dist/presentation/*" },
+    "#graph/*": { "@codegraph/source": "./src/graph/*", "default": "./dist/graph/*" },
+    "#mcp/*": { "@codegraph/source": "./src/mcp/*", "default": "./dist/mcp/*" },
+    "#ast-analysis/*": { "@codegraph/source": "./src/ast-analysis/*", "default": "./dist/ast-analysis/*" },
+    "#extractors/*": { "@codegraph/source": "./src/extractors/*", "default": "./dist/extractors/*" },
+    "#cli/*": { "@codegraph/source": "./src/cli/*", "default": "./dist/cli/*" },
+    "#types": { "@codegraph/source": "./src/types.ts", "default": "./dist/types.js" }
+  },
   "exports": {
     ".": {
       "import": "./dist/index.js",