@aroman22/codegraph-vba 1.17.1 → 2.0.0

package/README.md

@@ -2,11 +2,11 @@
 
 # CodeGraph (VBA & Access Fork)
 
-## 🎉 1.5 Released — VBA conditional-compilation is now correct + TempVars/RecordSource/RowSource indexed
+## v1.17.1 Released — Bounded Access Behavior Evidence and Layout-Aware Handler Lookup
 
 Already installed? Run `codegraph-vba upgrade` to update in place.
 
-Follow [@getcodegraph](https://x.com/getcodegraph) on X for updates.
+Follow the upstream project at [@getcodegraph](https://x.com/getcodegraph) on X for upstream updates.
 
 ### Supercharge Claude Code, Cursor, Codex, OpenCode, Hermes Agent, Gemini, Antigravity, and Kiro with Semantic Code Intelligence
 
@@ -18,7 +18,9 @@ Follow [@getcodegraph](https://x.com/getcodegraph) on X for updates.
 > This repository is a fork of the official [CodeGraph](https://github.com/colbymchenry/codegraph). 
 > It is renamed to **`codegraph-vba`** to avoid name collisions and features custom parser support for **VBA (Visual Basic for Applications)** and **MS Access** applications.
 
-### [Official Documentation & Website →](https://colbymchenry.github.io/codegraph/)
+### [Upstream Documentation & Website →](https://colbymchenry.github.io/codegraph/)
+
+> These pages describe upstream CodeGraph. Features added there after the integrated v1.4.1 base are not automatically available in this fork.
 
 [![Windows](https://img.shields.io/badge/Windows-supported-blue.svg)](#supported-platforms)
 [![macOS](https://img.shields.io/badge/macOS-supported-blue.svg)](#supported-platforms)
@@ -35,11 +37,11 @@ Follow [@getcodegraph](https://x.com/getcodegraph) on X for updates.
 
 <br>
 
-**The CodeGraph platform is coming** — for every PR, know exactly what to test, what could break, which flows are affected, and whether business logic is compromised.
+**The upstream CodeGraph platform is coming** — for every PR, know exactly what to test, what could break, which flows are affected, and whether business logic is compromised.
 
 <a href="https://getcodegraph.com"><img alt="Join the waitlist for early beta access" src="https://raw.githubusercontent.com/colbymchenry/codegraph/main/assets/waitlist.svg?v=2" height="52"></a>
 
-<sub>Get <b>early beta access</b> to the hosted product · <a href="https://getcodegraph.com">getcodegraph.com</a></sub>
+<sub>Get <b>early beta access</b> to the upstream hosted product · <a href="https://getcodegraph.com">getcodegraph.com</a></sub>
 
 </div>
 
@@ -47,7 +49,11 @@ Follow [@getcodegraph](https://x.com/getcodegraph) on X for updates.
 
 ## This is a fork — VBA / Access + Dysflow
 
-This repository is a fork of [`colbymchenry/codegraph`](https://github.com/colbymchenry/codegraph), maintained at [`ardelperal/codegraph-vba`](https://github.com/ardelperal/codegraph-vba). It is **identical to the upstream for every language except VBA / Access** — the fork adds nothing new to TypeScript, Python, Go, Rust, Java, etc., and is kept rebased against `colbymchenry/codegraph:main` so it stays current with upstream fixes and benchmarks.
+This repository is maintained at [`ardelperal/codegraph-vba`](https://github.com/ardelperal/codegraph-vba). It extends CodeGraph with VBA / Access analysis and fork-specific integration changes; it is not guaranteed identical to current upstream for other languages.
+
+The integrated upstream base is **v1.4.1**, commit [`ecc8b30`](https://github.com/colbymchenry/codegraph/commit/ecc8b307ac2f8a7d06bff02ee513c4ea2380b2f8), merged through [`910c7bb`](https://github.com/ardelperal/codegraph-vba/commit/910c7bb09fcc1e681e86803f93fffdb758086a22). Upstream v1.6.0 is not integrated. Fork and upstream versions are independent.
+
+See [fork capabilities and lineage](docs/fork-capabilities.md) for the delivered VBA, Access data/UI, error-analysis, and behavior-evidence scope.
 
 **Why fork?** To add VBA / Access language support that does not exist upstream, so agents can navigate Microsoft Access projects managed by Dysflow the same way they navigate TypeScript or Python today. See the [VBA / Access + Dysflow integration](#vba--access--dysflow-integration) section below for the feature spec, the pattern table, and the hard invariants.
 
@@ -70,7 +76,7 @@ pnpm run build            # produces dist/bin/codegraph.js
 # The binary is now at dist/bin/codegraph.js — point your agent's MCP at this path
 ```
 
-**If you do not need VBA / Access support**, install the upstream package instead — it is otherwise identical and gets released more frequently:
+**If you do not need VBA / Access support**, consider the upstream package instead. It follows its own release line; check its documentation rather than assuming feature parity:
 
 ```bash
 npm i -g @colbymchenry/codegraph
@@ -122,7 +128,7 @@ cd your-project
 codegraph-vba init
 ```
 
-<sub>`codegraph-vba init` creates the local `.codegraph-vba/` directory and builds the full graph in the same step — one command, done.</sub>
+<sub>`codegraph-vba init` creates the local `.codegraph/` directory and builds the full graph in the same step — one command, done.</sub>
 
 <div align="center">
 
@@ -142,7 +148,7 @@ Changed your mind? One command removes CodeGraph from every agent it configured:
 codegraph-vba uninstall
 ```
 
-<sub>Reverses the installer — strips CodeGraph's MCP server config, instructions, and permissions from each configured agent. Your project indexes (`.codegraph-vba/`) are left untouched; remove those per-project with `codegraph-vba uninit`. Use `--target` to remove from specific agents, or `--yes` to run non-interactively.</sub>
+<sub>Reverses the installer — strips CodeGraph's MCP server config, instructions, and permissions from each configured agent. Your project indexes (`.codegraph/`) are left untouched; remove those per-project with `codegraph-vba uninit`. Use `--target` to remove from specific agents, or `--yes` to run non-interactively.</sub>
 
 ---
 
@@ -589,7 +595,7 @@ codegraph-vba init
 
 Builds the per-project knowledge graph index, which then auto-syncs on every file change. A single global `codegraph-vba install` works in every project you open — no need to re-run the installer per project.
 
-That's it — your agent will use CodeGraph tools automatically when a `.codegraph-vba/` directory exists.
+That's it — your agent will use CodeGraph tools automatically when a `.codegraph/` directory exists.
 
 <details>
 <summary><strong>Manual Setup (Alternative)</strong></summary>
@@ -635,7 +641,7 @@ CodeGraph's MCP server delivers its usage guidance to your agent **automatically
 - **Answer structural questions directly with CodeGraph** — it *is* the pre-built index, so a grep/read loop just repeats work it already did. Treat the returned source as already read.
 - **Reach for `codegraph_explore` for almost anything** — "how does X work", a flow/"how does X reach Y", or surveying an area. One call returns the relevant symbols' verbatim source grouped by file, the call paths between them (dynamic-dispatch hops included), and a blast-radius summary. Name a file or symbol in the query to read its current line-numbered source.
 - **Trust the results — don't re-verify with grep**, and check the staleness banner after edits.
-- Works **per project**: query any project that has a `.codegraph-vba/` index by passing `projectPath` — so a monorepo where only some services are indexed, or a second repo, works in one session. A path with no index returns clean guidance to use built-in tools; indexing stays your decision.
+- Works **per project**: query any project that has a `.codegraph/` index by passing `projectPath` — so a monorepo where only some services are indexed, or a second repo, works in one session. A path with no index returns clean guidance to use built-in tools; indexing stays your decision.
 
 The exact text is `src/mcp/server-instructions.ts` — the single source of truth for the main agent. Because subagents and non-MCP harnesses never see the MCP guidance, the installer also writes a short marker-fenced section into the agent's instructions file pointing at the `codegraph-vba explore` CLI equivalent.
 
@@ -668,7 +674,7 @@ The exact text is `src/mcp/server-instructions.ts` — the single source of trut
 
 1. **Extraction** — [tree-sitter](https://tree-sitter.github.io/) parses source code into ASTs. Language-specific queries extract nodes (functions, classes, methods) and edges (calls, imports, extends, implements).
 
-2. **Storage** — Everything goes into a local SQLite database (`.codegraph-vba/codegraph.db`) with FTS5 full-text search.
+2. **Storage** — Everything goes into a local SQLite database (`.codegraph/codegraph.db`) with FTS5 full-text search.
 
 3. **Resolution** — After extraction, references are resolved: function calls → definitions, imports → source files, class inheritance, and framework-specific patterns.
 
@@ -744,7 +750,7 @@ When running as an MCP server, CodeGraph exposes a **single tool** — `codegrap
 
 The other tools (`codegraph_node`, `codegraph_search`, `codegraph_callers`, `codegraph_callees`, `codegraph_impact`, `codegraph_files`, `codegraph_status`, and the Access-specific `codegraph_behavior_evidence`) stay fully functional but **unlisted by default** — everything they return already arrives inline on `codegraph_explore` (its blast-radius section, the relationship map, a symbol's body as its callee list). Re-enable any of them for the MCP surface with the `CODEGRAPH_MCP_TOOLS` environment variable (e.g. `CODEGRAPH_MCP_TOOLS=explore,node,search,callers`), or use their CLI equivalents (`codegraph-vba node` / `query` / `callers` / `callees` / `impact` / `files` / `status`).
 
-Even when the server's own root has no `.codegraph-vba/` index, the tools stay available: pass `projectPath` to query any indexed project — a sub-service in a monorepo, or a second repo — in the same session. A path that has no index returns clean guidance to use built-in tools instead, so nothing fails loudly, and indexing stays your decision.
+Even when the server's own root has no `.codegraph/` index, the tools stay available: pass `projectPath` to query any indexed project — a sub-service in a monorepo, or a second repo — in the same session. A path that has no index returns clean guidance to use built-in tools instead, so nothing fails loudly, and indexing stays your decision.
 
 ---
 
@@ -967,7 +973,7 @@ Framework routing is validated the same way, on a canonical app per framework: E
 **MCP hits `database is locked`** — current builds shouldn't: CodeGraph bundles its own Node runtime and uses Node's built-in `node:sqlite` in WAL mode, where concurrent reads never block on a writer. If you still see it:
 
 - **You're on an old (pre-0.9) install.** Reinstall to get the bundled runtime — `curl -fsSL https://raw.githubusercontent.com/ardelperal/codegraph-vba/main/install.sh | sh` (macOS/Linux), `irm https://raw.githubusercontent.com/ardelperal/codegraph-vba/main/install.ps1 | iex` (Windows), or `npm i -g @aroman22/codegraph-vba@latest`.
-- **`codegraph-vba status` shows `Journal:` other than `wal`** — WAL couldn't be enabled on this filesystem (common on network shares and WSL2 `/mnt`), so reads can block on writes. Move the project (with its `.codegraph-vba/` folder) onto a local disk.
+- **`codegraph-vba status` shows `Journal:` other than `wal`** — WAL couldn't be enabled on this filesystem (common on network shares and WSL2 `/mnt`), so reads can block on writes. Move the project (with its `.codegraph/` folder) onto a local disk.
 
 **MCP server not connecting** — Your agent starts the server itself, so you don't launch it by hand. Make sure the project is initialized and indexed (`codegraph-vba status`) and that the path in your MCP config is correct. If it still won't connect, re-run `codegraph-vba install` to rewrite the config.
 
@@ -975,7 +981,7 @@ Framework routing is validated the same way, on a canonical app per framework: E
 
 **Missing symbols** — The MCP server auto-syncs on save (wait a couple seconds). Run `codegraph-vba sync` manually if needed. Check that the file's language is supported and isn't inside a `.gitignore`d or default-excluded directory (e.g. `node_modules`, `dist`).
 
-**Sharing one checkout between Windows and WSL** — Don't point both at the same `.codegraph-vba/`: the background-server lock and the SQLite index are tied to the OS that wrote them, and SQLite locking across the WSL2/Windows filesystem boundary is unreliable. Give each side its own index in the same tree by setting `CODEGRAPH_DIR` to a distinct name on one of them — e.g. `CODEGRAPH_DIR=.codegraph-win` on Windows, leaving WSL on the default `.codegraph-vba`. CodeGraph skips any sibling `.codegraph-*` directory when indexing and watching, so the two never trip over each other.
+**Sharing one checkout between Windows and WSL** — Don't point both at the same `.codegraph/`: the background-server lock and the SQLite index are tied to the OS that wrote them, and SQLite locking across the WSL2/Windows filesystem boundary is unreliable. Give each side its own index in the same tree by setting `CODEGRAPH_DIR` to a distinct name on one of them — e.g. `CODEGRAPH_DIR=.codegraph-win` on Windows, leaving WSL on the default `.codegraph`. CodeGraph skips any sibling `.codegraph-*` directory when indexing and watching, so the two never trip over each other.
 
 ## Star History
 

package/dist/directory.d.ts

@@ -36,7 +36,9 @@ export declare const CODEGRAPH_DIR: string;
  * default `.codegraph`, the active `CODEGRAPH_DIR` override, and any
  * `.codegraph-*` sibling. File-watching and the indexer skip ALL of these, so
  * when two environments share one working tree (Windows + WSL, issue #636)
- * neither indexes or watches the other's index directory.
+ * neither indexes or watches the other's index directory. The prefix match
+ * also covers the legacy `.codegraph-vba/` directory older releases of this
+ * fork wrote, so a stale one left in a consumer repo is never indexed.
  */
 export declare function isCodeGraphDataDir(name: string): boolean;
 /**

package/dist/extraction/frameworks/dysflow-export.d.ts

@@ -1,36 +1,33 @@
 /**
  * Dysflow-export framework resolver (issue #154).
  *
- * The 3 Dysflow-specific extractors ÔÇö form/report SaveAsText UI, test
- * manifests, and test sequences ÔÇö used to be hard-coded into
- * `extractFromSource` as a `detectedLanguage === 'vba' && <isFoo> (filePath)`
- * ladder. They are now lifted into this `FrameworkResolver`-shaped module
- * so they can be:
- *   1. Reached through the standard framework registry (the same path every
- *      other framework ÔÇö Express, React, Spring ÔÇö flows through).
- *   2. Opted out at the project level via `codegraph.json`'s
- *      `vba.dysflowExport: false` ÔÇö useful for projects that carry legacy
- *      `.form.txt`/`.report.txt` files (or test manifests from a different
- *      system) and want them tracked as just a `file` node instead of
- *      being expanded into the graph.
+ * Marks a project as "this is a Dysflow export" so `dysflow-export` shows up
+ * in the detected-framework list alongside Express, React, Spring and the
+ * rest. Detection is path-shape based: at least one `.form.txt` /
+ * `.report.txt` / `tests.*.json` / `sequences/*.json` in the tree, and no
+ * `vba.dysflowExport: false` opt-out in `codegraph.json`.
  *
- * Architecture: the underlying `VbaFormExtractor` / `VbaTestManifestExtractor`
- * / `VbaTestSequenceExtractor` classes are the single source of truth for
- * the per-file extraction logic. This module:
- *   - decides WHICH sub-extractor applies to a file (path shape);
- *   - delegates the actual `extract()` to that sub-extractor;
- *   - exposes the `FrameworkResolver` shape (`detect` / `extract` /
- *     `resolve` / `claimsReference`) so the rest of the codebase can treat
- *     "Dysflow export" as a regular framework on top of the base VBA
- *     language.
+ * PER-FILE EXTRACTION DOES NOT LIVE HERE (issue #314). The three Dysflow
+ * sub-extractors — `VbaFormExtractor`, `VbaTestManifestExtractor` and
+ * `VbaTestSequenceExtractor` — are dispatched by the VBA branch of
+ * `extractFromSource` in `../tree-sitter.ts`, gated on the `dysflowExport`
+ * flag that `loadDysflowExportConfig()` reads from the project config. That
+ * ladder is the ONLY dispatch site, and it runs on every path into
+ * extraction, including the ones that pass no `frameworkNames` at all
+ * (single-file re-index, library callers, the extraction unit tests).
  *
- * Behavior contract: with `dysflowExport: true` (the default), the emitted
- * nodes/edges/references are byte-identical to the pre-refactor paths in
- * `tree-sitter.ts`. With `dysflowExport: false`, the framework's `detect()`
- * returns `false` so it's never in the per-project detected list ÔÇö meaning
- * its `extract()` is never called and the form/report/manifest/sequence
- * files fall through to a `file`-only node via the language-specific
- * dispatch in `tree-sitter.ts`.
+ * This module deliberately exposes no `extract()`. It used to carry one that
+ * re-ran the same three sub-extractors, which meant every Dysflow artifact in
+ * a real project was parsed twice per index — once by the `tree-sitter.ts`
+ * ladder and once by the framework loop at the end of `extractFromSource` —
+ * and every manifest/sequence entry landed twice in `unresolved_refs`. Adding
+ * an `extract()` back here re-introduces that duplication; extend the
+ * `tree-sitter.ts` ladder instead.
+ *
+ * Opt-out contract: `vba.dysflowExport: false` turns BOTH halves off. This
+ * resolver's `detect()` returns `false` so the project is not classified as a
+ * Dysflow export, and the same config flag makes the `tree-sitter.ts` ladder
+ * emit a `file`-only node for the form/report/manifest/sequence shapes.
  */
 import { FrameworkResolver } from '../../resolution/types';
 export declare const dysflowExportResolver: FrameworkResolver;

package/dist/extraction/index.d.ts

@@ -53,6 +53,33 @@ export interface SyncResult {
  * Calculate SHA256 hash of file contents
  */
 export declare function hashContent(content: string): string;
+/**
+ * Issue #53: read extraction source with encoding-robust decode for VBA-family
+ * files (BOM strip + CP1252 fallback), byte-identical to the plain UTF-8 read
+ * for every other language. The same read must feed extraction, storage, and
+ * change-detection hashing so a BOM-carrying or CP1252 VBA file doesn't hash
+ * differently at detect-time than what was stored (perpetual "modified").
+ */
+/**
+ * Files that must be decoded with Access encoding rules (BOM strip + CP1252
+ * fallback) rather than as plain UTF-8.
+ *
+ * Two predicates because the family is matched two ways. `isVbaFamilyFile`
+ * owns the extensions (`.bas`, `.cls`, `.form.txt`, `.sql`, …). The Access
+ * structure export is `ERD/*.md`, so it is matched by PATH SHAPE — `.md`
+ * alone must never route every markdown file in a repo through the CP1252
+ * fallback — and that shape is owned by `grammars.ts` (issue #322).
+ *
+ * Combining them here rather than inside `isVbaFamilyFile` keeps
+ * `vba-source.ts` a leaf module: this is the only place that needs both.
+ *
+ * Without the ERD half, an export naming a table with accents decoded to
+ * replacement characters while the `.sql` and `.bas` referencing that same
+ * table decoded it correctly, so the ERD declaration never joined the
+ * placeholder those scanners emit and the table's field list hung off an
+ * orphan node.
+ */
+export declare function usesAccessEncoding(filePath: string): boolean;
 /**
  * An `ignore` matcher seeded with the built-in defaults, merged with the project's
  * root .gitignore so a negation there (e.g. `!vendor/`) overrides a default. Shared

package/dist/extraction/json-source.d.ts

@@ -0,0 +1,27 @@
+/**
+ * Decoding helpers for the JSON artifacts Dysflow writes beside a VBA export
+ * (`tests(.<slice>)*.json` test manifests, `sequences/*.json` test sequences).
+ *
+ * These are the only indexed files that are parsed as JSON rather than scanned
+ * as text, and they are deliberately NOT part of `isVbaFamilyFile` — JSON is
+ * UTF-8 by specification, so the CP1252 fallback in `readVbaSource` would turn
+ * a mis-encoded manifest into silently wrong data instead of a loud parse
+ * error. What they do share with the rest of the VBA family is the byte-order
+ * mark.
+ */
+/**
+ * Strip a leading UTF-8 BOM from already-decoded JSON text.
+ *
+ * A `.json` is read with a plain `fs.readFile(path, 'utf-8')`, and Node keeps
+ * the BOM as a leading `\uFEFF` rather than consuming it. `JSON.parse` rejects
+ * that character outright, so a BOM-carrying manifest used to contribute
+ * nothing to the graph but a `warning`-severity parse error — every `Test_*`
+ * link it declared silently vanished (issue #316). On Windows this is the
+ * common case, not an exotic one: PowerShell 5.1 writes the BOM by default for
+ * `-Encoding UTF8` in both `Set-Content` and `Out-File`.
+ *
+ * Only a BOM at position 0 is removed; a `\uFEFF` anywhere else is data and is
+ * left for `JSON.parse` to judge.
+ */
+export declare function stripJsonBom(text: string): string;
+//# sourceMappingURL=json-source.d.ts.map

package/dist/mcp/server-instructions.d.ts

@@ -17,7 +17,7 @@
  * tools (node/search/callers/…) stay defined and are re-enablable via
  * CODEGRAPH_MCP_TOOLS, but they are NOT listed to agents, so don't name them.
  */
-export declare const SERVER_INSTRUCTIONS = "# Codegraph \u2014 code intelligence over an indexed knowledge graph\n\nCodegraph is a SQLite knowledge graph of every symbol, edge, and file in\nthe workspace \u2014 pre-computed structure you would otherwise re-derive by\nreading files (cached intelligence: thousands of parse/trace decisions you\ndon't pay to re-reason each run). Reads are sub-millisecond; the index lags\nwrites by ~1s through the file watcher. Reach for it BEFORE *and* while\nwriting or editing code \u2014 not just for questions: one call returns the\nverbatim source PLUS who calls it and what it affects, so you edit with the\nblast radius in view. More accurate context, in far fewer tokens and\nround-trips than reading files yourself.\n\n## One tool: codegraph_explore \u2014 use it instead of reading files\n\nThere is a single tool, `codegraph_explore`, and it is Read-equivalent. It\ntakes either a natural-language question or a bag of symbol/file names and\nreturns the **verbatim, line-numbered source** of the relevant symbols\ngrouped by file \u2014 the same `<n>\\t<line>` shape `Read` gives you, safe to\n`Edit` from \u2014 PLUS the call path among them (including dynamic-dispatch hops\nlike callbacks, React re-render, and JSX children that grep can't follow) and\na blast-radius summary of what depends on them.\n\nWhether you're answering \"how does X work\" or implementing a change (fixing a\nbug, adding a feature), call `codegraph_explore` before you Read. ONE call\nusually answers the whole question. Codegraph IS the pre-built search index \u2014\nso running your own grep + read loop, or delegating the lookup to a separate\nfile-reading sub-task/agent, repeats work codegraph already did and costs more\nfor the same answer. A direct codegraph answer is typically one to a few\ncalls; a grep/read exploration is dozens.\n\n## How to query\n\n- **Almost any question \u2014 \"how does X work\", architecture, a bug, \"what/where is X\", or surveying an area** \u2192 `codegraph_explore` with a natural-language question or the relevant names. ONE capped call returns the verbatim source grouped by file; most often the ONLY call you need.\n- **\"How does X reach/become Y? / the flow / the path from X to Y\"** \u2192 `codegraph_explore`, naming the symbols that span the flow (e.g. `mutateElement renderScene`) \u2014 it surfaces the call path among them, riding dynamic-dispatch hops, and returns their source.\n- **Reading or editing a file/symbol you can name** \u2192 put its name or file path in the `codegraph_explore` query \u2014 it returns that current line-numbered source (safe to `Edit` from) with the call path and blast radius attached, so you don't Read it separately. For an overloaded name it returns every matching definition's body in one call.\n- **Need more?** Call `codegraph_explore` again with more specific names \u2014 treat the source it returns as already Read.\n\n## Anti-patterns\n\n- **Trust codegraph's results \u2014 don't re-verify them with grep.** They come from a full AST parse; re-checking with grep is slower, less accurate, and wastes context.\n- **Don't grep or Read first** to find or understand indexed code \u2014 ONE `codegraph_explore` returns the relevant symbols' source together in a single round-trip. Reach for raw `Read`/`Grep` only to confirm a specific detail codegraph didn't cover, or for what codegraph doesn't index (configs, docs).\n- **Don't reconstruct a flow by hand** \u2014 name the endpoints in one `codegraph_explore` and it surfaces the path between them, dynamic-dispatch hops included.\n- **After editing, check the staleness banner.** When a tool response starts with \"\u26A0\uFE0F Some files referenced below were edited since the last index sync\u2026\", the listed files are pending re-index \u2014 Read those specific files for accurate content. Every file NOT in that banner is fresh, so still trust codegraph. A different, rarer banner \u2014 \"\u26A0\uFE0F CodeGraph auto-sync is DISABLED\u2026\" \u2014 means live watching stopped entirely (the whole index is frozen, not just a few files); until it's resolved, Read files directly to confirm anything that may have changed.\n\n## Limitations\n\n- If a tool reports a project isn't indexed (no `.codegraph/`), stop calling codegraph tools for that project for the rest of the session and use your built-in tools there instead. Indexing is the user's decision \u2014 mention they can run `codegraph init` if it comes up, but don't run it yourself.\n- Index lags file writes by ~1 second.\n- Cross-file resolution is best-effort name matching; ambiguous calls may return multiple candidates.\n- No live correctness validation \u2014 that's still the TypeScript compiler / test suite / linter's job. Codegraph supplements those with structural context they don't have.\n\n## Supported Languages\n\nThe indexer recognizes a fixed set of languages; if you ask about symbols in a\nfile with an unsupported extension, codegraph will report the project isn't\nindexed for that file and you should fall back to Read/Grep. The fork-specific\naddition beyond upstream codegraph is **VBA / Access** (Dysflow export\nformat):\n\n- **VBA / Access** - Dysflow exports Access/VBA source as `.bas`/`.cls`/\n  `.form.txt`/`.report.txt`. Codegraph extracts `.bas`/`.cls` as `module`/\n  `class`/`function` nodes with `calls`/`implements`/`references` edges\n  (procedural-level; regex-based, not full AST). Cross-module calls, qualified\n  `Dim As`, `WithEvents`, and SQL table references inside string literals\n  emit synthesized edges tagged `metadata.synthesizedBy` (`vba-name-resolution`,\n  `vba-withevents`, `vba-sql-table`). A `.form.txt` / `.report.txt` emits a\n  `form-layout` / `report-layout` container, one\n  `form-instance-control` per named control, a `property` node per control\n  type, and a placeholder node per table/query it binds - but **no\n  procedures**: no `function`/`sub` node, and no class node for the form's\n  own code, comes from a layout file. The canonical code lives in the sibling\n  `.cls`, parsed by the same extractor on that file.\n- **Access event wiring has ONE direction: handler -> control/layout.** The\n  `event-handler` edge is stored from the handler procedure to the\n  `form-instance-control` it is named for (`btnSave_Click` -> `btnSave`), or\n  to the sibling layout node for a form/report lifecycle event\n  (`Form_Load` -> `Form_Orders`, carrying `metadata.scope: 'form'`). An\n  `=Expression()` event property resolves to the same direction, tagged\n  `vba-expression-handler`. There is no reverse edge: to answer \"what runs on\n  this control\", follow the edge BACKWARDS from the control. Scope every\n  control lookup by its layout - the same control name usually exists on\n  several forms, and a layout owns its controls through `contains`.\n- **A VBA call is not always a `calls` edge.** `Call Foo` and `Foo 1, 2` are\n  `calls`; a bare `Foo` on its own line could also be a `Const` read, so it\n  stays an ambiguous identifier and resolves to a `references` edge onto the\n  procedure. That bare form is the dominant call style in Access code-behind,\n  so a trace that follows only `calls` stops at the handler.\n- **Codegraph indexes the exported source tree, not the live `.accdb`.** It is\n  static evidence: it never proves a handler ran, and it says nothing about\n  whether the binary matches the export (Dysflow owns that round-trip). A\n  missing edge is missing evidence, not proof of no runtime effect.\n  Dysflow test manifests (`tests.*.json`) link each registered `Test_*`\n  procedure to its manifest with a `references` edge tagged\n  `vba-test-manifest` carrying the test name + tags, so `getCallers` of a\n  production symbol reaches its covering test atoms with the manifest and tags\n  to run.\n  Pass `projectPath` to a codegraph index that includes VBA files.\n- **VBA unresolved refs carry syntactic shape** (v1.7+). `unresolved_refs.reference_kind` is no longer the literal string `\"references\"` \u2014 it reports what the syntactic shape actually was. Values: `call` (paren-form or statement-form call site), `qualified-call` (`obj.Foo(...)` with runtime receiver), `property-get` / `property-set` (`Me.Name`, `obj.Prop = value`), `bang-get` / `bang-set` (`Me!SubCtl`, `obj!Field = value`), `unqualified-ident` (bare identifier like `HayErrorEnRiesgo` in an `If` condition), `member-with` (`.Member` inside a `With` block), `dao-query` (`DoCmd.OpenQuery \"X\"` argument). The legacy value `references` is retained on any path the round did not reclassify, so older SQL filters that key on it keep working. To find real missing callees, filter `WHERE reference_kind IN ('call','qualified-call','unqualified-ident','member-with','bang-get')` \u2014 that set has <10% false positives (DAO-field accesses, form-property reads, and bang refs no longer pollute the bucket).\n- **Post-extraction stub resolver** (v1.7+). Edges with `metadata.synthesizedBy='vba-name-resolution'` start life pointing at a synthetic function node; the resolver at `src/resolution/index.ts:resolveVbaCallStubs` (invoked from `indexAll` and `sync`) walks them and repoints each `target` to the real `nodes.id` when one exists. Runtime-object calls (`DAO.*`, `fso.*`, `ListBox.*`, `Collection.*`, `err.*`, `VBA.*`, `Application.*`, `Screen.*`, `DoCmd.*`, `CurrentDb.*`, `Forms`, `Reports`, `Debug`, `Modules`, `References`, `CommandBars`, `SysCmd`, `CreateObject`, `GetObject`, `Fields`) are explicitly declined \u2014 they remain `stub:true` because they can never link to user code. Shadow user classes (e.g. a user class actually named `DAO` with an `Execute` method) are preserved and linked normally. Every stub edge carries `metadata.repointDecision` with one of `reponted-to-real` (linked to a real `nodes.id`), `declined-runtime` (runtime object \u2014 never user code, filter OUT), `declined-ambiguous` (multiple real candidates \u2014 investigate), or `declined-not-found` (genuinely missing callee \u2014 this is the actionable signal). Consumers detecting \"missing callees\" MUST filter on `repointDecision='declined-not-found'`, NOT on the raw `stub=true` count \u2014 the raw count is dominated by runtime-object noise. See `docs/vba-stub-repoint-decision.md` for the full contract.\n";
+export declare const SERVER_INSTRUCTIONS = "# Codegraph \u2014 code intelligence over an indexed knowledge graph\n\nCodegraph is a SQLite knowledge graph of every symbol, edge, and file in\nthe workspace \u2014 pre-computed structure you would otherwise re-derive by\nreading files (cached intelligence: thousands of parse/trace decisions you\ndon't pay to re-reason each run). Reads are sub-millisecond; the index lags\nwrites by ~1s through the file watcher. Reach for it BEFORE *and* while\nwriting or editing code \u2014 not just for questions: one call returns the\nverbatim source PLUS who calls it and what it affects, so you edit with the\nblast radius in view. More accurate context, in far fewer tokens and\nround-trips than reading files yourself.\n\n## One tool: codegraph_explore \u2014 use it instead of reading files\n\nThere is a single tool, `codegraph_explore`, and it is Read-equivalent. It\ntakes either a natural-language question or a bag of symbol/file names and\nreturns the **verbatim, line-numbered source** of the relevant symbols\ngrouped by file \u2014 the same `<n>\\t<line>` shape `Read` gives you, safe to\n`Edit` from \u2014 PLUS the call path among them (including dynamic-dispatch hops\nlike callbacks, React re-render, and JSX children that grep can't follow) and\na blast-radius summary of what depends on them.\n\nWhether you're answering \"how does X work\" or implementing a change (fixing a\nbug, adding a feature), call `codegraph_explore` before you Read. ONE call\nusually answers the whole question. Codegraph IS the pre-built search index \u2014\nso running your own grep + read loop, or delegating the lookup to a separate\nfile-reading sub-task/agent, repeats work codegraph already did and costs more\nfor the same answer. A direct codegraph answer is typically one to a few\ncalls; a grep/read exploration is dozens.\n\n## How to query\n\n- **Almost any question \u2014 \"how does X work\", architecture, a bug, \"what/where is X\", or surveying an area** \u2192 `codegraph_explore` with a natural-language question or the relevant names. ONE capped call returns the verbatim source grouped by file; most often the ONLY call you need.\n- **\"How does X reach/become Y? / the flow / the path from X to Y\"** \u2192 `codegraph_explore`, naming the symbols that span the flow (e.g. `mutateElement renderScene`) \u2014 it surfaces the call path among them, riding dynamic-dispatch hops, and returns their source.\n- **Reading or editing a file/symbol you can name** \u2192 put its name or file path in the `codegraph_explore` query \u2014 it returns that current line-numbered source (safe to `Edit` from) with the call path and blast radius attached, so you don't Read it separately. For an overloaded name it returns every matching definition's body in one call.\n- **Need more?** Call `codegraph_explore` again with more specific names \u2014 treat the source it returns as already Read.\n\n## Anti-patterns\n\n- **Trust codegraph's results \u2014 don't re-verify them with grep.** They come from a full AST parse; re-checking with grep is slower, less accurate, and wastes context.\n- **Don't grep or Read first** to find or understand indexed code \u2014 ONE `codegraph_explore` returns the relevant symbols' source together in a single round-trip. Reach for raw `Read`/`Grep` only to confirm a specific detail codegraph didn't cover, or for what codegraph doesn't index (configs, docs).\n- **Don't reconstruct a flow by hand** \u2014 name the endpoints in one `codegraph_explore` and it surfaces the path between them, dynamic-dispatch hops included.\n- **After editing, check the staleness banner.** When a tool response starts with \"\u26A0\uFE0F Some files referenced below were edited since the last index sync\u2026\", the listed files are pending re-index \u2014 Read those specific files for accurate content. Every file NOT in that banner is fresh, so still trust codegraph. A different, rarer banner \u2014 \"\u26A0\uFE0F CodeGraph auto-sync is DISABLED\u2026\" \u2014 means live watching stopped entirely (the whole index is frozen, not just a few files); until it's resolved, Read files directly to confirm anything that may have changed.\n\n## Limitations\n\n- If a tool reports a project isn't indexed (no `.codegraph/`), stop calling codegraph tools for that project for the rest of the session and use your built-in tools there instead. Indexing is the user's decision \u2014 mention they can run `codegraph init` if it comes up, but don't run it yourself.\n- Index lags file writes by ~1 second.\n- Cross-file resolution is best-effort name matching; ambiguous calls may return multiple candidates.\n- No live correctness validation \u2014 that's still the TypeScript compiler / test suite / linter's job. Codegraph supplements those with structural context they don't have.\n\n## Supported Languages\n\nThe indexer recognizes a fixed set of languages; if you ask about symbols in a\nfile with an unsupported extension, codegraph will report the project isn't\nindexed for that file and you should fall back to Read/Grep. The fork-specific\naddition beyond upstream codegraph is **VBA / Access** (Dysflow export\nformat):\n\n- **VBA / Access** - Dysflow exports Access/VBA source as `.bas`/`.cls`/\n  `.form.txt`/`.report.txt`. Codegraph extracts `.bas`/`.cls` as `module`/\n  `class`/`function` nodes with `calls`/`implements`/`references` edges\n  (procedural-level; regex-based, not full AST). Cross-module calls, qualified\n  `Dim As`, `WithEvents`, and SQL table references inside string literals\n  emit synthesized edges tagged `metadata.synthesizedBy` (`vba-name-resolution`,\n  `vba-withevents`, `vba-sql-table`). A `.form.txt` / `.report.txt` emits a\n  `form-layout` / `report-layout` container, one\n  `form-instance-control` per named control, a `property` node per control\n  type, and a placeholder node per table/query it binds - but **no\n  procedures**: no `function`/`sub` node, and no class node for the form's\n  own code, comes from a layout file. The canonical code lives in the sibling\n  `.cls`, parsed by the same extractor on that file.\n- **Access event wiring has ONE direction: handler -> control/layout.** The\n  `event-handler` edge is stored from the handler procedure to the\n  `form-instance-control` it is named for (`btnSave_Click` -> `btnSave`), or\n  to the sibling layout node for a form/report lifecycle event\n  (`Form_Load` -> `Form_Orders`, carrying `metadata.scope: 'form'`). An\n  `=Expression()` event property resolves to the same direction, tagged\n  `vba-expression-handler`. There is no reverse edge: to answer \"what runs on\n  this control\", follow the edge BACKWARDS from the control. Scope every\n  control lookup by its layout - the same control name usually exists on\n  several forms, and a layout owns its controls through `contains`.\n- **A VBA call is not always a `calls` edge.** `Call Foo` and `Foo 1, 2` are\n  `calls`; a bare `Foo` on its own line could also be a `Const` read, so it\n  stays an ambiguous identifier and resolves to a `references` edge onto the\n  procedure. That bare form is the dominant call style in Access code-behind,\n  so a trace that follows only `calls` stops at the handler.\n- **Codegraph indexes the exported source tree, not the live `.accdb`.** It is\n  static evidence: it never proves a handler ran, and it says nothing about\n  whether the binary matches the export (Dysflow owns that round-trip). A\n  missing edge is missing evidence, not proof of no runtime effect.\n  Dysflow test manifests (`tests.*.json`) link each registered `Test_*`\n  procedure to its manifest with a `references` edge tagged\n  `vba-test-manifest` carrying the test name + tags, so `getCallers` of a\n  production symbol reaches its covering test atoms with the manifest and tags\n  to run.\n  Pass `projectPath` to a codegraph index that includes VBA files.\n- **Saved Access queries are first-class nodes \u2014 do not grep the `.sql`.** A\n  Dysflow-exported `queries/<Name>.sql` whose directory also carries a\n  `queries.json` manifest becomes a `query` node (language `sql`, named after\n  the file) with a `references` edge to every table its `FROM` / `JOIN` /\n  `INTO` / `UPDATE` names, tagged `sql-query-table`; a table that resolves to\n  another backend file is tagged `vba-external-backend` instead. A `.sql` with\n  no sibling `queries.json` is deliberately NOT indexed, so an ordinary SQL\n  migration in a non-Access repo stays out of the graph.\n- **Dysflow test sequences sit beside the manifests.** A `sequences/*.json`\n  emits a `file` node and one `references` edge per `procedures[]` entry to\n  that `Test_*` procedure, tagged `vba-test-sequence` and carrying\n  `runnerPolicy`, `sequenceFile` and `procedureIndex`. So `getCallers` of a\n  test atom reaches both the manifest that registers it (`vba-test-manifest`)\n  and the sequence that orders it, with the runner policy to honour.\n- **Table structure comes from the Access ERD export.** An `ERD/*.md` produced\n  by the Access structure generator emits one `class` node per table (tagged\n  `access-erd-table`), one `type_member` per field joined by `contains`, and a\n  `references` edge from a linked table to the backend it really lives in\n  (tagged `vba-linked-table`). This is the cheapest answer to \"what columns\n  does this table have\" and to \"which backend owns it\" \u2014 ask codegraph before\n  reading the export. The extractor requires the generated header, so a\n  hand-written diagram in an `ERD/` folder contributes nothing.\n- **VBA unresolved refs carry syntactic shape** (v1.7+). `unresolved_refs.reference_kind` is no longer the literal string `\"references\"` \u2014 it reports what the syntactic shape actually was. Values: `call` (paren-form or statement-form call site), `qualified-call` (`obj.Foo(...)` with runtime receiver), `property-get` / `property-set` (`Me.Name`, `obj.Prop = value`), `bang-get` / `bang-set` (`Me!SubCtl`, `obj!Field = value`), `unqualified-ident` (bare identifier like `HayErrorEnRiesgo` in an `If` condition), `member-with` (`.Member` inside a `With` block), `dao-query` (`DoCmd.OpenQuery \"X\"` argument). The legacy value `references` is retained on any path the round did not reclassify, so older SQL filters that key on it keep working. To find real missing callees, filter `WHERE reference_kind IN ('call','qualified-call','unqualified-ident','member-with','bang-get')` \u2014 that set has <10% false positives (DAO-field accesses, form-property reads, and bang refs no longer pollute the bucket).\n- **Post-extraction stub resolver** (v1.7+). Edges with `metadata.synthesizedBy='vba-name-resolution'` start life pointing at a synthetic function node; the resolver at `src/resolution/index.ts:resolveVbaCallStubs` (invoked from `indexAll` and `sync`) walks them and repoints each `target` to the real `nodes.id` when one exists. Runtime-object calls (`DAO.*`, `fso.*`, `ListBox.*`, `Collection.*`, `err.*`, `VBA.*`, `Application.*`, `Screen.*`, `DoCmd.*`, `CurrentDb.*`, `Forms`, `Reports`, `Debug`, `Modules`, `References`, `CommandBars`, `SysCmd`, `CreateObject`, `GetObject`, `Fields`) are explicitly declined \u2014 they remain `stub:true` because they can never link to user code. Shadow user classes (e.g. a user class actually named `DAO` with an `Execute` method) are preserved and linked normally. Every stub edge carries `metadata.repointDecision` with one of `reponted-to-real` (linked to a real `nodes.id`), `declined-runtime` (runtime object \u2014 never user code, filter OUT), `declined-ambiguous` (multiple real candidates \u2014 investigate), or `declined-not-found` (genuinely missing callee \u2014 this is the actionable signal). Consumers detecting \"missing callees\" MUST filter on `repointDecision='declined-not-found'`, NOT on the raw `stub=true` count \u2014 the raw count is dominated by runtime-object noise. See `docs/vba-stub-repoint-decision.md` for the full contract.\n";
 /**
  * Instructions variant sent when the server's own root has NO codegraph index.
  *

package/dist/sync/watcher.d.ts

@@ -237,6 +237,20 @@ export declare class FileWatcher {
      * as they are during a full index.
      */
     private isDysflowQuerySql;
+    /**
+     * True when `rel` is a Dysflow saved-query manifest (`queries.json`).
+     *
+     * The manifest is not itself indexable, but it is the gate that decides
+     * whether the `.sql` files beside it are Access saved queries at all — both
+     * here and in the indexer's directory discovery. Without this check a
+     * manifest write schedules nothing (#318): a first export that writes its
+     * `.sql` files before the manifest leaves every query out of the graph,
+     * because those `.sql` events were dropped for having no manifest yet and
+     * the manifest that would have made them indexable is not a source file.
+     * Treating the manifest as a change closes the race from both directions —
+     * the sync it schedules picks up every `.sql` in that directory.
+     */
+    private isDysflowQueriesManifest;
     /**
      * Shared change handler for both watch strategies. `rel` is a
      * project-relative POSIX path. Applies the ignore + source-file filters and,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@aroman22/codegraph-vba",
-  "version": "1.17.1",
+  "version": "2.0.0",
   "description": "Local-first code intelligence for AI agents (MCP). Self-contained — bundles its own runtime.",
   "bin": {
     "codegraph-vba": "npm-shim.js"
@@ -15,12 +15,12 @@
     "./package.json": "./package.json"
   },
   "optionalDependencies": {
-    "@aroman22/codegraph-vba-darwin-arm64": "1.17.1",
-    "@aroman22/codegraph-vba-darwin-x64": "1.17.1",
-    "@aroman22/codegraph-vba-linux-arm64": "1.17.1",
-    "@aroman22/codegraph-vba-linux-x64": "1.17.1",
-    "@aroman22/codegraph-vba-win32-arm64": "1.17.1",
-    "@aroman22/codegraph-vba-win32-x64": "1.17.1"
+    "@aroman22/codegraph-vba-darwin-arm64": "2.0.0",
+    "@aroman22/codegraph-vba-darwin-x64": "2.0.0",
+    "@aroman22/codegraph-vba-linux-arm64": "2.0.0",
+    "@aroman22/codegraph-vba-linux-x64": "2.0.0",
+    "@aroman22/codegraph-vba-win32-arm64": "2.0.0",
+    "@aroman22/codegraph-vba-win32-x64": "2.0.0"
   },
   "files": [
     "npm-shim.js",