@optave/codegraph 3.11.2 → 3.13.0

package/README.md

@@ -43,7 +43,7 @@ Codegraph builds a function-level dependency graph of your entire codebase — e
 
 It parses your code with [tree-sitter](https://tree-sitter.github.io/) (native Rust or WASM), stores the graph in SQLite, and exposes it where it matters most:
 
-- **MCP server** — AI agents query the graph directly through 30 tools — one call instead of 30 `grep`/`find`/`cat` invocations
+- **MCP server** — AI agents query the graph directly through 34 tools — one call instead of dozens of `grep`/`find`/`cat` invocations
 - **CLI** — developers and agents explore, query, and audit code from the terminal
 - **CI gates** — `check` and `manifesto` commands enforce quality thresholds with exit codes
 - **Programmatic API** — embed codegraph in your own tools via `npm install`
@@ -76,7 +76,7 @@ No config files, no Docker, no JVM, no API keys, no accounts. Point your agent a
 
 ### Feature comparison
 
-<sub>Comparison last verified: May 2026. Claims verified against each repo's README/docs. Full analysis: <a href="generated/competitive/COMPETITIVE_ANALYSIS.md">COMPETITIVE_ANALYSIS.md</a></sub>
+<sub>Comparison last verified: June 2026. Claims verified against each repo's README/docs. Full analysis: <a href="generated/competitive/COMPETITIVE_ANALYSIS.md">COMPETITIVE_ANALYSIS.md</a></sub>
 
 | Capability | codegraph (this repo) | [code-review-graph](https://github.com/tirth8205/code-review-graph) | [narsil-mcp](https://github.com/postrv/narsil-mcp) | [codegraph (other)¹](https://github.com/colbymchenry/codegraph) | [axon](https://github.com/harshkedia177/axon) | [GitNexus](https://github.com/abhigyanpatwari/GitNexus) |
 |---|:---:|:---:|:---:|:---:|:---:|:---:|
@@ -100,7 +100,7 @@ No config files, no Docker, no JVM, no API keys, no accounts. Point your agent a
 
 | | Differentiator | In practice |
 |---|---|---|
-| **🤖** | **AI-first architecture** | 30-tool [MCP server](https://modelcontextprotocol.io/) — agents query the graph directly instead of scraping the filesystem. One call replaces 20+ grep/find/cat invocations |
+| **🤖** | **AI-first architecture** | 34-tool [MCP server](https://modelcontextprotocol.io/) — agents query the graph directly instead of scraping the filesystem. One call replaces 20+ grep/find/cat invocations |
 | **🏷️** | **Role classification** | Every symbol auto-tagged as `entry`/`core`/`utility`/`adapter`/`dead`/`leaf` — agents understand a symbol's architectural role without reading surrounding code |
 | **🔬** | **Function-level, not just files** | Traces `handleAuth()` → `validateToken()` → `decryptJWT()` and shows 14 callers across 9 files break if `decryptJWT` changes |
 | **⚡** | **Always-fresh graph** | Three-tier change detection: journal (O(changed)) → mtime+size (O(n) stats) → hash (O(changed) reads). Sub-second rebuilds — agents work with current data |
@@ -124,10 +124,10 @@ That's it. The graph is ready. Now connect your AI agent.
 
 ### For AI agents (primary use case)
 
-Connect directly via MCP — your agent gets 30 tools to query the graph:
+Connect directly via MCP — your agent gets 34 tools to query the graph:
 
 ```bash
-codegraph mcp          # 33-tool MCP server — AI queries the graph directly
+codegraph mcp          # 34-tool MCP server — AI queries the graph directly
 ```
 
 Or add codegraph to your agent's instructions (e.g. `CLAUDE.md`):
@@ -169,7 +169,7 @@ cd codegraph && npm install && npm link
 
 | | Feature | Description |
 |---|---|---|
-| 🤖 | **MCP server** | 33-tool MCP server for AI assistants; single-repo by default, opt-in multi-repo |
+| 🤖 | **MCP server** | 34-tool MCP server for AI assistants; single-repo by default, opt-in multi-repo |
 | 🎯 | **Deep context** | `context` gives agents source, deps, callers, signature, and tests for a function in one call; `audit --quick` gives structural summaries |
 | 🏷️ | **Node role classification** | Every symbol auto-tagged as `entry`/`core`/`utility`/`adapter`/`dead`/`leaf` based on connectivity — agents instantly know architectural role |
 | 📦 | **Batch querying** | Accept a list of targets and return all results in one JSON payload — enables multi-agent parallel dispatch |
@@ -332,6 +332,7 @@ Composite commands for risk-driven workflows and multi-agent dispatch.
 codegraph audit <file-or-function>    # Combined structural summary + impact + health in one report
 codegraph audit <target> --quick      # Structural summary only (skip impact and health)
 codegraph audit src/queries.js -T     # Audit all functions in a file
+codegraph explain <target>            # Alias for audit — same output, easier to discover
 codegraph triage                      # Ranked audit priority queue (connectivity + hotspots + roles)
 codegraph triage -T --limit 20        # Top 20 riskiest functions, excluding tests
 codegraph triage --level file -T      # File-level hotspot analysis
@@ -456,6 +457,22 @@ codegraph registry remove <name>  # Unregister
 
 `codegraph build` auto-registers the project — no manual setup needed.
 
+### Configuration
+
+Inspect and manage `.codegraphrc.json` settings.
+
+```bash
+codegraph config                    # Show all config keys with values and sources
+codegraph config --json             # JSON output of the merged config
+codegraph config --init             # Scaffold a .codegraphrc.json with all sections pre-populated
+codegraph config --edit             # Open .codegraphrc.json in $EDITOR
+codegraph config --enable-global    # Opt this repo into user-level global config
+codegraph config --disable-global   # Opt this repo out of user-level global config
+codegraph config --list-global      # Show the contents of the global config file
+```
+
+A user-level config file at `~/.config/codegraph/config.json` (XDG) or `~/.codegraph/config.json` lets you set personal defaults once and apply them to opted-in repos. The merge order is: DEFAULTS → global (if consented) → project → env. Non-interactive contexts (CI, MCP) never apply the global config without explicit consent. See [docs/guides/configuration.md](docs/guides/configuration.md) for full details.
+
 ### Common Flags
 
 | Flag | Description |
@@ -475,6 +492,8 @@ codegraph registry remove <name>  # Unregister
 | `--limit <n>` | Limit number of results |
 | `--offset <n>` | Skip first N results (pagination) |
 | `--rrf-k <n>` | RRF smoothing constant for multi-query search (default 60) |
+| `--user-config [path]` | Apply global user config for this run; optionally specify a custom path instead of the XDG default (`~/.config/codegraph/config.json`) |
+| `--no-user-config` | Skip global user config for this run (CI/non-interactive safe) |
 
 ## 🌐 Language Support
 
@@ -624,36 +643,38 @@ Codegraph also extracts symbols from common callback patterns: Commander `.comma
 
 Self-measured on every release via CI ([build benchmarks](generated/benchmarks/BUILD-BENCHMARKS.md) | [embedding benchmarks](generated/benchmarks/EMBEDDING-BENCHMARKS.md) | [query benchmarks](generated/benchmarks/QUERY-BENCHMARKS.md) | [incremental benchmarks](generated/benchmarks/INCREMENTAL-BENCHMARKS.md) | [resolution precision/recall](tests/benchmarks/resolution/)):
 
-*Last updated: v3.11.1 (2026-05-30)*
+*Last updated: v3.12.0 (2026-06-11)*
 
 | Metric | Native | WASM |
 |---|---|---|
-| Build speed | **3.7 ms/file** | **18.4 ms/file** |
-| Query time | **34ms** | **46ms** |
-| No-op rebuild | **24ms** | **20ms** |
-| 1-file rebuild | **81ms** | **68ms** |
-| Query: fn-deps | **2.5ms** | **2.3ms** |
-| Query: path | **2.5ms** | **2.3ms** |
-| ~50,000 files (est.) | **~185.0s build** | **~920.0s build** |
-| Resolution precision | **89.9%** | — |
-| Resolution recall | **42.3%** | — |
-
-Metrics are normalized per file for cross-version comparability. Times above are for a full initial build — incremental rebuilds only re-parse changed files.
+| Build speed | **4.4 ms/file** | **21.2 ms/file** |
+| Query time | **38ms** | **48ms** |
+| No-op rebuild | **30ms** | **27ms** |
+| 1-file rebuild | **121ms** | **76ms** |
+| Query: fn-deps | **2.7ms** | **2.6ms** |
+| Query: path | **2.8ms** | **2.5ms** |
+| ~50,000 files (est.) | **~220.0s build** | **~1060.0s build** |
+| Resolution precision | **84.4%** | — |
+| Resolution recall | **56.1%** | — |
+
+Metrics are normalized per file for cross-version comparability. Times above are for a full initial build — incremental rebuilds only re-parse changed files. v3.12.0 note: native build speed regressed ~22% (3.6→4.4 ms/file) and native 1-file incremental rebuild regressed ~41% (86→121 ms); tracked in [#1446](https://github.com/optave/ops-codegraph-tool/issues/1446).
 
 <details><summary>Per-language resolution precision/recall</summary>
 
+v3.12.0 note: global precision dropped 89.9%→84.4%, driven by new false positives in `elixir` (+17 FP), `julia` (+11 FP), and `objc` (+5 FP) — all three still have 0% recall; tracked in [#1447](https://github.com/optave/ops-codegraph-tool/issues/1447). Global recall improved substantially (42.3%→56.1%).
+
 | Language | Precision | Recall | TP | FP | FN | Edges | Dynamic |
 |----------|----------:|-------:|---:|---:|---:|------:|--------:|
-| javascript | 100.0% | 66.7% | 12 | 0 | 6 | 18 | 14/28 |
-| typescript | 100.0% | 75.0% | 15 | 0 | 5 | 20 | — |
+| javascript | 100.0% | 97.6% | 41 | 0 | 1 | 42 | 14/32 |
+| typescript | 100.0% | 100.0% | 47 | 0 | 0 | 47 | — |
 | bash | 100.0% | 100.0% | 12 | 0 | 0 | 12 | 0/1 |
 | c | 100.0% | 100.0% | 9 | 0 | 0 | 9 | — |
 | clojure | 80.0% | 26.7% | 4 | 1 | 11 | 15 | — |
 | cpp | 100.0% | 57.1% | 8 | 0 | 6 | 14 | — |
-| csharp | 100.0% | 52.6% | 10 | 0 | 9 | 19 | — |
+| csharp | 100.0% | 100.0% | 23 | 0 | 0 | 23 | — |
 | cuda | 50.0% | 33.3% | 4 | 4 | 8 | 12 | — |
 | dart | 0.0% | 0.0% | 0 | 0 | 18 | 18 | — |
-| elixir | 0.0% | 0.0% | 0 | 0 | 21 | 21 | — |
+| elixir | 0.0% | 0.0% | 0 | 17 | 21 | 21 | — |
 | erlang | 100.0% | 100.0% | 12 | 0 | 0 | 12 | — |
 | fsharp | 0.0% | 0.0% | 0 | 11 | 12 | 12 | — |
 | gleam | 100.0% | 26.7% | 4 | 0 | 11 | 15 | — |
@@ -661,18 +682,19 @@ Metrics are normalized per file for cross-version comparability. Times above are
 | groovy | 100.0% | 7.7% | 1 | 0 | 12 | 13 | — |
 | haskell | 100.0% | 33.3% | 4 | 0 | 8 | 12 | — |
 | hcl | 0.0% | 0.0% | 0 | 0 | 2 | 2 | — |
-| java | 100.0% | 52.9% | 9 | 0 | 8 | 17 | — |
-| julia | 0.0% | 0.0% | 0 | 0 | 15 | 15 | — |
+| java | 100.0% | 76.5% | 13 | 0 | 4 | 17 | — |
+| julia | 0.0% | 0.0% | 0 | 11 | 15 | 15 | — |
 | kotlin | 92.3% | 63.2% | 12 | 1 | 7 | 19 | — |
 | lua | 100.0% | 15.4% | 2 | 0 | 11 | 13 | — |
-| objc | 0.0% | 0.0% | 0 | 1 | 12 | 12 | — |
+| objc | 0.0% | 0.0% | 0 | 6 | 12 | 12 | — |
 | ocaml | 100.0% | 8.3% | 1 | 0 | 11 | 12 | — |
-| php | 100.0% | 31.6% | 6 | 0 | 13 | 19 | — |
+| php | 100.0% | 57.9% | 11 | 0 | 8 | 19 | — |
+| pts-javascript | 100.0% | 100.0% | 13 | 0 | 0 | 13 | — |
 | python | 100.0% | 60.0% | 9 | 0 | 6 | 15 | 15/15 |
 | r | 100.0% | 100.0% | 11 | 0 | 0 | 11 | — |
 | ruby | 100.0% | 100.0% | 11 | 0 | 0 | 11 | 11/11 |
-| rust | 100.0% | 35.7% | 5 | 0 | 9 | 14 | — |
-| scala | 100.0% | 71.4% | 5 | 0 | 2 | 7 | — |
+| rust | 100.0% | 64.3% | 9 | 0 | 5 | 14 | — |
+| scala | 100.0% | 100.0% | 7 | 0 | 0 | 7 | — |
 | solidity | 33.3% | 7.7% | 1 | 2 | 12 | 13 | — |
 | swift | 75.0% | 42.9% | 6 | 2 | 8 | 14 | 9/9 |
 | tsx | 100.0% | 100.0% | 13 | 0 | 0 | 13 | — |
@@ -683,13 +705,25 @@ Metrics are normalized per file for cross-version comparability. Times above are
 
 | Mode | Resolved | Expected | Recall |
 |------|--------:|---------:|-------:|
+| receiver-typed | 32 | 112 | 28.6% |
 | module-function | 16 | 112 | 14.3% |
-| receiver-typed | 17 | 104 | 16.3% |
-| static | 66 | 93 | 71.0% |
-| same-file | 48 | 86 | 55.8% |
-| interface-dispatched | 7 | 12 | 58.3% |
-| class-inheritance | 0 | 4 | 0.0% |
+| static | 78 | 96 | 81.3% |
+| same-file | 66 | 90 | 73.3% |
+| interface-dispatched | 19 | 19 | 100.0% |
+| class-inheritance | 8 | 12 | 66.7% |
+| callback | 7 | 7 | 100.0% |
+| pts-spread | 4 | 4 | 100.0% |
+| pts-define-property | 3 | 3 | 100.0% |
+| dynamic | 3 | 3 | 100.0% |
+| pts-create-prototype | 2 | 2 | 100.0% |
+| points-to | 1 | 2 | 50.0% |
+| re-export | 2 | 2 | 100.0% |
+| pts-for-of | 2 | 2 | 100.0% |
+| pts-set | 2 | 2 | 100.0% |
+| pts-array-from | 2 | 2 | 100.0% |
 | trait-dispatch | 0 | 2 | 0.0% |
+| define-property | 1 | 1 | 100.0% |
+| defineProperty-accessor | 1 | 1 | 100.0% |
 | package-function | 1 | 1 | 100.0% |
 
 </details>
@@ -712,7 +746,7 @@ Optional: `@huggingface/transformers` (semantic search), `@modelcontextprotocol/
 
 ### MCP Server
 
-Codegraph is built around a [Model Context Protocol](https://modelcontextprotocol.io/) server with 30 tools (31 in multi-repo mode) — the primary way agents consume the graph:
+Codegraph is built around a [Model Context Protocol](https://modelcontextprotocol.io/) server with 34 tools (35 in multi-repo mode) — the primary way agents consume the graph:
 
 ```bash
 codegraph mcp                  # Single-repo mode (default) — only local project
@@ -782,6 +816,8 @@ Copy `.github/workflows/codegraph-impact.yml` to your repo, and every PR will ge
 
 Create a `.codegraphrc.json` in your project root to customize behavior. The snippets below cover the most-used keys — see **[docs/guides/configuration.md](docs/guides/configuration.md)** for the full reference (every group, every key, every default).
 
+**Global (user-level) config:** you can also define personal defaults once at `~/.config/codegraph/config.json` and opt individual repos into it with `codegraph config --enable-global`. The global layer merges below the project config so repos always win, and non-interactive contexts (CI, MCP) never apply it without explicit consent. See [docs/guides/configuration.md#user-level-global-configuration](docs/guides/configuration.md#user-level-global-configuration).
+
 ```json
 {
   "include": ["src/**", "lib/**"],
@@ -842,7 +878,7 @@ Works with any secret manager: 1Password CLI (`op`), Bitwarden (`bw`), `pass`, H
 
 ### MCP tool filtering
 
-Codegraph's MCP server exposes 30+ tools by default. For models with a small context window, you can shrink the schema by disabling tools you don't use:
+Codegraph's MCP server exposes 34 tools by default. For models with a small context window, you can shrink the schema by disabling tools you don't use:
 
 ```json
 {
@@ -900,7 +936,7 @@ const { results: fused } = await multiSearchData(
 
 ## ⚠️ Limitations
 
-- **No TypeScript type-checker integration** — type inference resolves annotations, `new` expressions, and assignment chains, but does not invoke `tsc` for overload resolution or complex generics
+- **TypeScript compiler integration is auto-enabled** — when `typescript` is installed and a `tsconfig.json` is found, the TypeScript compiler API pass runs automatically; disable with `"build": { "typescriptResolver": false }` in `.codegraphrc.json` if you want faster builds without it; heuristic type inference (annotations, `new` expressions, assignment chains) is always active as a baseline
 - **Dynamic calls are best-effort** — complex computed property access and `eval` patterns are not resolved
 - **Python imports** — resolves relative imports but doesn't follow `sys.path` or virtual environment packages
 - **Dataflow analysis** — intraprocedural (single-function scope), not interprocedural
@@ -918,7 +954,7 @@ See **[ROADMAP.md](docs/roadmap/ROADMAP.md)** for the full development roadmap a
 7. ~~**TypeScript Migration**~~ — **Complete** (v3.4.0) — all 271 source files migrated from JS to TS, zero `.js` remaining
 8. ~~**Native Analysis Acceleration**~~ — **Complete** (v3.5.0) — all build phases in Rust/rusqlite, sub-100ms incremental rebuilds, better-sqlite3 lazy-loaded as fallback only
 9. ~~**Expanded Language Support**~~ — **Complete** (v3.8.0) — 23 new languages in 4 batches (11 → 34), dual-engine WASM + Rust support for all
-10. **Analysis Depth** — TypeScript-native resolution, inter-procedural type propagation, field-based points-to analysis
+10. ~~**Analysis Depth**~~ — **Complete** (v3.12.0) — TypeScript-native resolution, inter-procedural type propagation, field-based points-to analysis, barrel re-export chain resolution, CHA+RTA dynamic dispatch
 11. **Runtime & Extensibility** — event-driven pipeline, plugin system, query caching, pagination
 12. **Quality, Security & Technical Debt** — supply-chain security (SBOM, SLSA), CI coverage gates, timer cleanup, tech debt kill list
 13. **Intelligent Embeddings** — LLM-generated descriptions, enhanced embeddings, module summaries

package/dist/cli/commands/audit.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"audit.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/audit.ts"],"names":[],"mappings":"AAKA,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,aAAa,CAAC;AAErD,eAAO,MAAM,OAAO,EAAE,iBAwCrB,CAAC"}

package/dist/cli/commands/audit.js

@@ -5,7 +5,8 @@ import { explain } from '../../presentation/queries-cli.js';
 import { config } from '../shared/options.js';
 export const command = {
     name: 'audit <target>',
-    description: 'Composite report: explain + impact + health metrics per function',
+    alias: 'explain',
+    description: 'Composite report: explain + impact + health metrics per function (alias: explain)',
     options: [
         ['-d, --db <path>', 'Path to graph.db'],
         ['--quick', 'Structural summary only (skip impact analysis and health metrics)'],

package/dist/cli/commands/audit.js.map

@@ -1 +1 @@
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+{"version":3,"file":"audit.js","sourceRoot":"","sources":["../../../src/cli/commands/audit.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,MAAM,2BAA2B,CAAC;AACxD,OAAO,EAAE,iBAAiB,EAAE,MAAM,yBAAyB,CAAC;AAC5D,OAAO,EAAE,KAAK,EAAE,MAAM,6BAA6B,CAAC;AACpD,OAAO,EAAE,OAAO,EAAE,MAAM,mCAAmC,CAAC;AAC5D,OAAO,EAAE,MAAM,EAAE,MAAM,sBAAsB,CAAC;AAG9C,MAAM,CAAC,MAAM,OAAO,GAAsB;IACxC,IAAI,EAAE,gBAAgB;IACtB,KAAK,EAAE,SAAS;IAChB,WAAW,EAAE,mFAAmF;IAChG,OAAO,EAAE;QACP,CAAC,iBAAiB,EAAE,kBAAkB,CAAC;QACvC,CAAC,SAAS,EAAE,mEAAmE,CAAC;QAChF,CAAC,aAAa,EAAE,sBAAsB,EAAE,GAAG,CAAC;QAC5C,CAAC,mBAAmB,EAAE,2CAA2C,EAAE,WAAW,CAAC;QAC/E,CAAC,mBAAmB,EAAE,uBAAuB,CAAC;QAC9C,CAAC,gBAAgB,EAAE,sCAAsC,CAAC;QAC1D,CAAC,iBAAiB,EAAE,yDAAyD,CAAC;QAC9E,CAAC,YAAY,EAAE,gBAAgB,CAAC;QAChC,CAAC,sBAAsB,EAAE,oCAAoC,CAAC;QAC9D,CAAC,mBAAmB,EAAE,6BAA6B,CAAC;QACpD,CAAC,UAAU,EAAE,4CAA4C,CAAC;KAC3D;IACD,QAAQ,CAAC,CAAC,OAAO,CAAC,EAAE,IAAI;QACtB,IAAI,IAAI,CAAC,IAAI,IAAI,CAAE,iBAAuC,CAAC,QAAQ,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;YAC/E,OAAO,iBAAiB,IAAI,CAAC,IAAI,aAAa,iBAAiB,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;QAC/E,CAAC;IACH,CAAC;IACD,OAAO,CAAC,CAAC,MAAM,CAAC,EAAE,IAAI,EAAE,GAAG;QACzB,MAAM,KAAK,GAAG,GAAG,CAAC,gBAAgB,CAAC,IAAI,CAAC,CAAC;QACzC,IAAI,IAAI,CAAC,KAAK,EAAE,CAAC;YACf,OAAO,CAAC,MAAO,EAAE,IAAI,CAAC,EAAE,EAAE;gBACxB,KAAK,EAAE,QAAQ,CAAC,IAAI,CAAC,KAAe,EAAE,EAAE,CAAC;gBACzC,GAAG,KAAK;aACT,CAAC,CAAC;YACH,OAAO;QACT,CAAC;QACD,KAAK,CAAC,MAAO,EAAE,IAAI,CAAC,EAAE,EAAE;YACtB,KAAK,EAAE,QAAQ,CAAC,IAAI,CAAC,KAAe,EAAE,EAAE,CAAC;YACzC,IAAI,EAAE,IAAI,CAAC,IAAI;YACf,IAAI,EAAE,IAAI,CAAC,IAAI;YACf,OAAO,EAAE,KAAK,CAAC,OAAO;YACtB,IAAI,EAAE,KAAK,CAAC,IAAI;YAChB,MAAM;SACP,CAAC,CAAC;IACL,CAAC;CACF,CAAC"}

package/dist/cli/commands/batch.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"batch.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/batch.ts"],"names":[],"mappings":"AAMA,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,aAAa,CAAC;AAErD,eAAO,MAAM,OAAO,EAAE,iBAwDrB,CAAC"}
+{"version":3,"file":"batch.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/batch.ts"],"names":[],"mappings":"AAMA,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,aAAa,CAAC;AAErD,eAAO,MAAM,OAAO,EAAE,iBAyDrB,CAAC"}

package/dist/cli/commands/batch.js

@@ -16,6 +16,7 @@ export const command = {
         ['-k, --kind <kind>', 'Filter by symbol kind'],
         ['-T, --no-tests', 'Exclude test/spec files from results'],
         ['--include-tests', 'Include test/spec files (overrides excludeTests config)'],
+        ['-j, --json', 'Accepted for script compatibility (batch always outputs JSON)'],
     ],
     validate([_command, _targets], opts) {
         if (opts.kind && !EVERY_SYMBOL_KIND.includes(opts.kind)) {

package/dist/cli/commands/batch.js.map

@@ -1 +1 @@
-{"version":3,"file":"batch.js","sourceRoot":"","sources":["../../../src/cli/commands/batch.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,SAAS,CAAC;AACzB,OAAO,EAAE,WAAW,EAAE,MAAM,2BAA2B,CAAC;AACxD,OAAO,EAAE,iBAAiB,EAAE,MAAM,yBAAyB,CAAC;AAC5D,OAAO,EAAE,cAAc,EAAE,YAAY,EAAE,MAAM,yBAAyB,CAAC;AACvE,OAAO,EAAE,UAAU,EAAE,MAAM,6BAA6B,CAAC;AACzD,OAAO,EAAE,WAAW,EAAE,cAAc,EAAE,MAAM,wBAAwB,CAAC;AAGrE,MAAM,CAAC,MAAM,OAAO,GAAsB;IACxC,IAAI,EAAE,8BAA8B;IACpC,WAAW,EAAE,6FAA6F,MAAM,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE;IAClJ,OAAO,EAAE;QACP,CAAC,iBAAiB,EAAE,kBAAkB,CAAC;QACvC,CAAC,oBAAoB,EAAE,0DAA0D,CAAC;QAClF,CAAC,SAAS,EAAE,sCAAsC,CAAC;QACnD,CAAC,aAAa,EAAE,8CAA8C,CAAC;QAC/D,CAAC,mBAAmB,EAAE,2CAA2C,EAAE,WAAW,CAAC;QAC/E,CAAC,mBAAmB,EAAE,uBAAuB,CAAC;QAC9C,CAAC,gBAAgB,EAAE,sCAAsC,CAAC;QAC1D,CAAC,iBAAiB,EAAE,yDAAyD,CAAC;KAC/E;IACD,QAAQ,CAAC,CAAC,QAAQ,EAAE,QAAQ,CAAC,EAAE,IAAI;QACjC,IAAI,IAAI,CAAC,IAAI,IAAI,CAAE,iBAAuC,CAAC,QAAQ,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;YAC/E,OAAO,iBAAiB,IAAI,CAAC,IAAI,aAAa,iBAAiB,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;QAC/E,CAAC;IACH,CAAC;IACD,KAAK,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,iBAAiB,CAAC,EAAE,IAAI,EAAE,GAAG;QACnD,IAAI,OAAkB,CAAC;QACvB,IAAI,CAAC;YACH,IAAI,IAAI,CAAC,QAAQ,EAAE,CAAC;gBAClB,MAAM,GAAG,GAAG,EAAE,CAAC,YAAY,CAAC,IAAI,CAAC,QAAkB,EAAE,OAAO,CAAC,CAAC,IAAI,EAAE,CAAC;gBACrE,IAAI,GAAG,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC;oBACxB,OAAO,GAAG,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC;gBAC5B,CAAC;qBAAM,CAAC;oBACN,OAAO,GAAG,GAAG,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC;gBAC/C,CAAC;YACH,CAAC;iBAAM,IAAI,IAAI,CAAC,KAAK,EAAE,CAAC;gBACtB,MAAM,MAAM,GAAa,EAAE,CAAC;gBAC5B,IAAI,KAAK,EAAE,MAAM,KAAK,IAAI,OAAO,CAAC,KAAK;oBAAE,MAAM,CAAC,IAAI,CAAC,KAAe,CAAC,CAAC;gBACtE,MAAM,GAAG,GAAG,MAAM,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,QAAQ,CAAC,OAAO,CAAC,CAAC,IAAI,EAAE,CAAC;gBAC3D,OAAO,GAAG,GAAG,CAAC,UAAU,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC;YACvF,CAAC;iBAAM,CAAC;gBACN,OAAO,GAAG,YAAY,CAAC,iBAAwC,CAAC,CAAC;YACnE,CAAC;QACH,CAAC;QAAC,OAAO,GAAY,EAAE,CAAC;YACtB,MAAM,IAAI,WAAW,CAAC,4BAA4B,cAAc,CAAC,GAAG,CAAC,EAAE,EAAE;gBACvE,KAAK,EAAE,GAAY;aACpB,CAAC,CAAC;QACL,CAAC;QAED,IAAI,CAAC,OAAO,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACrC,MAAM,IAAI,WAAW,CACnB,0EAA0E,CAC3E,CAAC;QACJ,CAAC;QAED,UAAU,CAAC,OAA8D,EAAE,IAAI,CAAC,EAAE,EAAE;YAClF,OAAO;YACP,KAAK,EAAE,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,QAAQ,CAAC,IAAI,CAAC,KAAe,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS;YAClE,IAAI,EAAE,IAAI,CAAC,IAAI;YACf,IAAI,EAAE,IAAI,CAAC,IAAI;YACf,OAAO,EAAE,GAAG,CAAC,cAAc,CAAC,IAAI,CAAC;SAClC,CAAC,CAAC;IACL,CAAC;CACF,CAAC"}
+{"version":3,"file":"batch.js","sourceRoot":"","sources":["../../../src/cli/commands/batch.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,SAAS,CAAC;AACzB,OAAO,EAAE,WAAW,EAAE,MAAM,2BAA2B,CAAC;AACxD,OAAO,EAAE,iBAAiB,EAAE,MAAM,yBAAyB,CAAC;AAC5D,OAAO,EAAE,cAAc,EAAE,YAAY,EAAE,MAAM,yBAAyB,CAAC;AACvE,OAAO,EAAE,UAAU,EAAE,MAAM,6BAA6B,CAAC;AACzD,OAAO,EAAE,WAAW,EAAE,cAAc,EAAE,MAAM,wBAAwB,CAAC;AAGrE,MAAM,CAAC,MAAM,OAAO,GAAsB;IACxC,IAAI,EAAE,8BAA8B;IACpC,WAAW,EAAE,6FAA6F,MAAM,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE;IAClJ,OAAO,EAAE;QACP,CAAC,iBAAiB,EAAE,kBAAkB,CAAC;QACvC,CAAC,oBAAoB,EAAE,0DAA0D,CAAC;QAClF,CAAC,SAAS,EAAE,sCAAsC,CAAC;QACnD,CAAC,aAAa,EAAE,8CAA8C,CAAC;QAC/D,CAAC,mBAAmB,EAAE,2CAA2C,EAAE,WAAW,CAAC;QAC/E,CAAC,mBAAmB,EAAE,uBAAuB,CAAC;QAC9C,CAAC,gBAAgB,EAAE,sCAAsC,CAAC;QAC1D,CAAC,iBAAiB,EAAE,yDAAyD,CAAC;QAC9E,CAAC,YAAY,EAAE,+DAA+D,CAAC;KAChF;IACD,QAAQ,CAAC,CAAC,QAAQ,EAAE,QAAQ,CAAC,EAAE,IAAI;QACjC,IAAI,IAAI,CAAC,IAAI,IAAI,CAAE,iBAAuC,CAAC,QAAQ,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;YAC/E,OAAO,iBAAiB,IAAI,CAAC,IAAI,aAAa,iBAAiB,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;QAC/E,CAAC;IACH,CAAC;IACD,KAAK,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,iBAAiB,CAAC,EAAE,IAAI,EAAE,GAAG;QACnD,IAAI,OAAkB,CAAC;QACvB,IAAI,CAAC;YACH,IAAI,IAAI,CAAC,QAAQ,EAAE,CAAC;gBAClB,MAAM,GAAG,GAAG,EAAE,CAAC,YAAY,CAAC,IAAI,CAAC,QAAkB,EAAE,OAAO,CAAC,CAAC,IAAI,EAAE,CAAC;gBACrE,IAAI,GAAG,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC;oBACxB,OAAO,GAAG,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC;gBAC5B,CAAC;qBAAM,CAAC;oBACN,OAAO,GAAG,GAAG,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC;gBAC/C,CAAC;YACH,CAAC;iBAAM,IAAI,IAAI,CAAC,KAAK,EAAE,CAAC;gBACtB,MAAM,MAAM,GAAa,EAAE,CAAC;gBAC5B,IAAI,KAAK,EAAE,MAAM,KAAK,IAAI,OAAO,CAAC,KAAK;oBAAE,MAAM,CAAC,IAAI,CAAC,KAAe,CAAC,CAAC;gBACtE,MAAM,GAAG,GAAG,MAAM,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,QAAQ,CAAC,OAAO,CAAC,CAAC,IAAI,EAAE,CAAC;gBAC3D,OAAO,GAAG,GAAG,CAAC,UAAU,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC;YACvF,CAAC;iBAAM,CAAC;gBACN,OAAO,GAAG,YAAY,CAAC,iBAAwC,CAAC,CAAC;YACnE,CAAC;QACH,CAAC;QAAC,OAAO,GAAY,EAAE,CAAC;YACtB,MAAM,IAAI,WAAW,CAAC,4BAA4B,cAAc,CAAC,GAAG,CAAC,EAAE,EAAE;gBACvE,KAAK,EAAE,GAAY;aACpB,CAAC,CAAC;QACL,CAAC;QAED,IAAI,CAAC,OAAO,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACrC,MAAM,IAAI,WAAW,CACnB,0EAA0E,CAC3E,CAAC;QACJ,CAAC;QAED,UAAU,CAAC,OAA8D,EAAE,IAAI,CAAC,EAAE,EAAE;YAClF,OAAO;YACP,KAAK,EAAE,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,QAAQ,CAAC,IAAI,CAAC,KAAe,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS;YAClE,IAAI,EAAE,IAAI,CAAC,IAAI;YACf,IAAI,EAAE,IAAI,CAAC,IAAI;YACf,OAAO,EAAE,GAAG,CAAC,cAAc,CAAC,IAAI,CAAC;SAClC,CAAC,CAAC;IACL,CAAC;CACF,CAAC"}

package/dist/cli/commands/build.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"build.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/build.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,aAAa,CAAC;AAErD,eAAO,MAAM,OAAO,EAAE,iBAwBrB,CAAC"}
+{"version":3,"file":"build.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/build.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,aAAa,CAAC;AAErD,eAAO,MAAM,OAAO,EAAE,iBA6BrB,CAAC"}

package/dist/cli/commands/build.js

@@ -13,7 +13,10 @@ export const command = {
     ],
     async execute([dir], opts, ctx) {
         const root = path.resolve(dir || '.');
-        const engine = ctx.program.opts().engine;
+        const globalOpts = ctx.program.opts();
+        const engine = globalOpts.engine;
+        // Prompt for global-config consent on interactive TTY builds (§4.3).
+        const promptForConsent = !process.env.CI && !!process.stdin.isTTY && !!process.stdout.isTTY;
         await buildGraph(root, {
             incremental: opts.incremental,
             ast: opts.ast,
@@ -22,6 +25,8 @@ export const command = {
             dataflow: opts.dataflow,
             cfg: opts.cfg,
             dbPath: opts.db ? path.resolve(opts.db) : undefined,
+            userConfig: globalOpts.userConfig,
+            promptForConsent,
         });
     },
 };

package/dist/cli/commands/build.js.map

@@ -1 +1 @@
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package/dist/cli/commands/config.d.ts

@@ -0,0 +1,3 @@
+import type { CommandDefinition } from '../types.js';
+export declare const command: CommandDefinition;
+//# sourceMappingURL=config.d.ts.map

package/dist/cli/commands/config.d.ts.map

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package/dist/cli/commands/config.js

@@ -0,0 +1,272 @@
+import { spawnSync } from 'node:child_process';
+import fs from 'node:fs';
+import path from 'node:path';
+import { clearConfigCache, DEFAULTS, getDefaultUserConfigPath, loadConfig, loadConfigWithProvenance, resolveUserConfigPath, } from '../../infrastructure/config.js';
+import { getUserConfigConsent, listUserConfigConsent, REGISTRY_PATH, setUserConfigConsent, } from '../../infrastructure/registry.js';
+import { formatTable } from '../../presentation/table.js';
+/**
+ * Recursively flatten a nested config object to dot-notation key/value pairs.
+ * Arrays and null values are serialised to strings.
+ */
+function flattenConfig(obj, prefix = '') {
+    const out = [];
+    for (const [k, v] of Object.entries(obj)) {
+        const fullKey = prefix ? `${prefix}.${k}` : k;
+        if (v !== null && typeof v === 'object' && !Array.isArray(v)) {
+            out.push(...flattenConfig(v, fullKey));
+        }
+        else if (Array.isArray(v)) {
+            out.push({ key: fullKey, value: v.length === 0 ? '[]' : JSON.stringify(v) });
+        }
+        else {
+            out.push({ key: fullKey, value: v === null ? 'null' : String(v) });
+        }
+    }
+    return out;
+}
+/**
+ * Expand a top-level provenance map (e.g. { build: 'project' }) to cover every
+ * flattened dot-notation key (e.g. 'build.incremental' → 'project').
+ */
+function expandProvenance(flatEntries, provenance) {
+    const map = new Map();
+    for (const { key } of flatEntries) {
+        // Provenance is keyed by top-level section (e.g. 'build', 'llm'), so
+        // extract the first segment to find the governing provenance entry.
+        const topLevel = key.split('.')[0] ?? key;
+        map.set(key, provenance[topLevel] ?? 'default');
+    }
+    return map;
+}
+/**
+ * Render the effective config as a human-readable Key/Value/Source table.
+ * All rows are shown, sorted so non-default overrides appear first, then
+ * remaining defaults alphabetically.
+ */
+function renderConfigTable(config, provenance) {
+    const flat = flattenConfig(config);
+    const sourceMap = expandProvenance(flat, provenance);
+    // Show all entries — sorting non-defaults first, then alphabetically
+    const rows = flat
+        .slice()
+        .sort((a, b) => {
+        const sa = sourceMap.get(a.key) ?? 'default';
+        const sb = sourceMap.get(b.key) ?? 'default';
+        // Non-defaults first
+        if (sa !== 'default' && sb === 'default')
+            return -1;
+        if (sa === 'default' && sb !== 'default')
+            return 1;
+        return a.key.localeCompare(b.key);
+    })
+        .map(({ key, value }) => [key, value, sourceMap.get(key) ?? 'default']);
+    const keyWidth = Math.max(3, ...rows.map((r) => r[0].length));
+    const valWidth = Math.max(5, ...rows.map((r) => r[1].length));
+    // Source column is always short ('default', 'user', 'project', 'env')
+    const srcWidth = 7;
+    return `${formatTable({
+        columns: [
+            { header: 'Key', width: keyWidth },
+            { header: 'Value', width: valWidth },
+            { header: 'Source', width: srcWidth },
+        ],
+        rows: rows,
+        indent: 0,
+    })}\n`;
+}
+/**
+ * Build a scaffolded global config JSON file.
+ * Produces valid JSON with common sections pre-populated at their defaults.
+ * Uses DEFAULTS so the values always reflect the current schema.
+ *
+ * All keys are optional — users can delete sections they don't need.
+ */
+function buildInitTemplate() {
+    // Build a plain object — no comments in JSON, but keep it self-explanatory.
+    // Unknown top-level keys are silently ignored by mergeConfig.
+    const template = {
+        // LLM provider for AI features (codegraph explain, context, etc.)
+        // Use apiKeyCommand to pull the key from a secret manager at runtime.
+        // Scope to specific repos with:
+        //   { "appliesTo": ["~/projects/*"], "config": { ... } }
+        llm: {
+            provider: DEFAULTS.llm.provider,
+            model: DEFAULTS.llm.model,
+            baseUrl: DEFAULTS.llm.baseUrl,
+            apiKey: DEFAULTS.llm.apiKey,
+            apiKeyCommand: DEFAULTS.llm.apiKeyCommand,
+        },
+        query: {
+            defaultDepth: DEFAULTS.query.defaultDepth,
+            defaultLimit: DEFAULTS.query.defaultLimit,
+            excludeTests: DEFAULTS.query.excludeTests,
+        },
+        build: {
+            incremental: DEFAULTS.build.incremental,
+            typescriptResolver: DEFAULTS.build.typescriptResolver,
+        },
+        ci: {
+            failOnCycles: DEFAULTS.ci.failOnCycles,
+            impactThreshold: DEFAULTS.ci.impactThreshold,
+        },
+        search: {
+            defaultMinScore: DEFAULTS.search.defaultMinScore,
+            topK: DEFAULTS.search.topK,
+        },
+    };
+    return `${JSON.stringify(template, null, 2)}\n`;
+}
+export const command = {
+    name: 'config',
+    description: 'Show or manage codegraph configuration (project + user-level global config)',
+    options: [
+        ['-j, --json', 'Output as JSON'],
+        ['--explain', 'Show per-key provenance (default / user / project / env)'],
+        ['--enable-global', 'Record consent to apply the global config to this repo'],
+        ['--disable-global', 'Record consent to skip the global config for this repo'],
+        ['--list-global', 'List all repos with a recorded consent decision'],
+        [
+            '--init',
+            'Scaffold a global config file at the default XDG location with all sections pre-populated',
+        ],
+        ['--edit', 'Open the global config file in $EDITOR (prints the path if $EDITOR is unset)'],
+    ],
+    execute(_args, opts, ctx) {
+        const rootDir = path.resolve('.');
+        // ── Init: scaffold global config ───────────────────────────────────
+        if (opts.init) {
+            const targetPath = getDefaultUserConfigPath();
+            if (fs.existsSync(targetPath)) {
+                process.stderr.write(`Global config already exists at ${targetPath}\n` +
+                    `Run \`codegraph config --edit\` to open it, or delete it and re-run --init.\n`);
+                process.exit(1);
+            }
+            fs.mkdirSync(path.dirname(targetPath), { recursive: true });
+            fs.writeFileSync(targetPath, buildInitTemplate(), 'utf-8');
+            process.stdout.write(`Created global config at ${targetPath}\n`);
+            process.stdout.write(`Next steps:\n` +
+                `  1. Edit the file: codegraph config --edit\n` +
+                `  2. Enable it for this repo: codegraph config --enable-global\n`);
+            return;
+        }
+        // ── Edit: open global config in $EDITOR ────────────────────────────
+        if (opts.edit) {
+            // Prefer the existing file; fall back to the default path so the user
+            // can create-and-edit in one step even before running --init.
+            const filePath = resolveUserConfigPath() ?? getDefaultUserConfigPath();
+            const editor = process.env.EDITOR || process.env.VISUAL;
+            if (!editor) {
+                process.stdout.write(`${filePath}\n`);
+                process.stderr.write(`$EDITOR is not set. Set it in your shell profile (e.g. export EDITOR=nano)\n` +
+                    `or open the file manually at the path printed above.\n`);
+                return;
+            }
+            // Ensure the directory exists so the editor can create the file
+            fs.mkdirSync(path.dirname(filePath), { recursive: true });
+            const result = spawnSync(editor, [filePath], { stdio: 'inherit' });
+            if (result.error) {
+                process.stderr.write(`Failed to launch editor "${editor}": ${result.error.message}\n`);
+                process.exit(1);
+            }
+            if (result.status !== 0) {
+                process.exit(result.status ?? 1);
+            }
+            return;
+        }
+        // ── Consent management ─────────────────────────────────────────────
+        if (opts.enableGlobal) {
+            setUserConfigConsent(rootDir, 'enabled');
+            clearConfigCache();
+            const globalPath = resolveUserConfigPath();
+            if (!globalPath) {
+                process.stderr.write(`Consent recorded: "enabled" for ${rootDir}\n` +
+                    `Note: no global config file found. Create one at ~/.config/codegraph/config.json\n`);
+            }
+            else {
+                process.stderr.write(`Consent recorded: "enabled" for ${rootDir}\n` + `Global config: ${globalPath}\n`);
+            }
+            return;
+        }
+        if (opts.disableGlobal) {
+            setUserConfigConsent(rootDir, 'disabled');
+            clearConfigCache();
+            process.stderr.write(`Consent recorded: "disabled" for ${rootDir}\n`);
+            return;
+        }
+        if (opts.listGlobal) {
+            const entries = listUserConfigConsent(REGISTRY_PATH);
+            if (opts.json) {
+                process.stdout.write(`${JSON.stringify(entries, null, 2)}\n`);
+                return;
+            }
+            if (entries.length === 0) {
+                process.stdout.write('No repos have a recorded global-config consent decision.\n');
+                return;
+            }
+            process.stdout.write('Global config consent decisions:\n\n');
+            for (const { path: p, decision } of entries) {
+                process.stdout.write(`  ${decision === 'enabled' ? '✔' : '✘'} ${decision.padEnd(8)} ${p}\n`);
+            }
+            return;
+        }
+        // ── Explain mode ───────────────────────────────────────────────────
+        if (opts.explain) {
+            const { config, provenance, appliedGlobalPath, consentDecision } = loadConfigWithProvenance(rootDir, {
+                userConfig: ctx.program.opts().userConfig,
+            });
+            const globalPath = resolveUserConfigPath();
+            const consent = getUserConfigConsent(rootDir);
+            if (opts.json) {
+                process.stdout.write(`${JSON.stringify({
+                    config,
+                    provenance,
+                    appliedGlobalPath,
+                    globalFilePath: globalPath,
+                    consentDecision: consentDecision ?? consent ?? 'undecided',
+                }, null, 2)}\n`);
+                return;
+            }
+            // Human-readable explain output
+            process.stdout.write('=== Codegraph config provenance ===\n\n');
+            const consentStr = consentDecision ?? consent ?? 'undecided';
+            process.stdout.write(`Global config file : ${globalPath ?? '(none found)'}\n`);
+            process.stdout.write(`Applied this run   : ${appliedGlobalPath ? 'yes' : 'no'}\n`);
+            process.stdout.write(`Consent for repo   : ${consentStr}\n`);
+            process.stdout.write(`  (change with \`codegraph config --enable-global\` or \`--disable-global\`)\n`);
+            if (!globalPath) {
+                process.stdout.write(`\nDiscovery hint: create a global config at ~/.config/codegraph/config.json\n` +
+                    `then run \`codegraph config --enable-global\` in repos where you want it applied.\n`);
+            }
+            else if (!appliedGlobalPath) {
+                process.stdout.write(`\nDiscovery hint: global config exists but is not applied to this repo.\n` +
+                    `Run \`codegraph config --enable-global\` to enable it here.\n`);
+            }
+            process.stdout.write('\n--- Per-key provenance ---\n\n');
+            const provenanceEntries = Object.entries(provenance).sort(([a], [b]) => a.localeCompare(b));
+            for (const [key, source] of provenanceEntries) {
+                process.stdout.write(`  ${source.padEnd(8)} ${key}\n`);
+            }
+            return;
+        }
+        // ── Default: print effective config ────────────────────────────────
+        const globalPath = resolveUserConfigPath();
+        const consent = getUserConfigConsent(rootDir);
+        if (opts.json) {
+            const config = loadConfig(rootDir, { userConfig: ctx.program.opts().userConfig });
+            process.stdout.write(`${JSON.stringify(config, null, 2)}\n`);
+        }
+        else {
+            // Human-readable table: Key | Value | Source
+            const { config, provenance } = loadConfigWithProvenance(rootDir, {
+                userConfig: ctx.program.opts().userConfig,
+            });
+            process.stdout.write(renderConfigTable(config, provenance));
+            if (globalPath && !consent) {
+                process.stderr.write(`\nℹ Global config found at ${globalPath} — not applied to this repo.\n` +
+                    `  Run \`codegraph config --enable-global\` to opt in, or\n` +
+                    `  \`codegraph config --disable-global\` to dismiss this notice.\n`);
+            }
+        }
+    },
+};
+//# sourceMappingURL=config.js.map