projscan 3.7.0 → 4.0.0

package/README.md

@@ -9,9 +9,9 @@
 
 **Agent-first code intelligence.** An MCP server that lets AI coding agents (Claude Code, Codex, Cursor, Gemini, Windsurf, Cline, Continue, Zed — any MCP-aware client) query your codebase — with a CLI for humans and a local plugin layer for team-specific policy and reporting.
 
-[AI Agent Quick Start](#ai-agent-integration-mcp) · [CLI Quick Start](#quick-start) · [Commands](#commands) · [Full Guide](https://github.com/abhiyoheswaran1/projscan/blob/v3.7.0/docs/GUIDE.md) · [Roadmap](https://github.com/abhiyoheswaran1/projscan/blob/v3.7.0/docs/ROADMAP.md)
+[AI Agent Quick Start](#ai-agent-integration-mcp) · [CLI Quick Start](#quick-start) · [Commands](#commands) · [Full Guide](https://github.com/abhiyoheswaran1/projscan/blob/v4.0.0/docs/GUIDE.md) · [Roadmap](https://github.com/abhiyoheswaran1/projscan/blob/v4.0.0/docs/ROADMAP.md)
 
-<img src="https://raw.githubusercontent.com/abhiyoheswaran1/projscan/v3.7.0/docs/projscan-reporter-plugin.png" alt="projscan reporter plugin running in a macOS-style terminal window with a team health summary" width="700">
+<img src="https://raw.githubusercontent.com/abhiyoheswaran1/projscan/v4.0.0/docs/projscan-reporter-plugin.png" alt="projscan reporter plugin running in a macOS-style terminal window with a team health summary" width="700">
 
 </div>
 
@@ -33,7 +33,7 @@ The local plugin platform lets teams add project-specific findings and render `d
 npx projscan
 ```
 
-<img src="https://raw.githubusercontent.com/abhiyoheswaran1/projscan/v3.7.0/docs/projscan-reporter-plugin.gif" alt="projscan doctor rendered through a local reporter plugin in a macOS-style terminal window" width="700">
+<img src="https://raw.githubusercontent.com/abhiyoheswaran1/projscan/v4.0.0/docs/projscan-reporter-plugin.gif" alt="projscan doctor rendered through a local reporter plugin in a macOS-style terminal window" width="700">
 
 Run `projscan doctor` for a focused health check:
 
@@ -41,7 +41,7 @@ Run `projscan doctor` for a focused health check:
 npx projscan doctor
 ```
 
-<img src="https://raw.githubusercontent.com/abhiyoheswaran1/projscan/v3.7.0/docs/npx%20projscan%20doctor.gif" alt="npx projscan doctor" width="700">
+<img src="https://raw.githubusercontent.com/abhiyoheswaran1/projscan/v4.0.0/docs/npx%20projscan%20doctor.gif" alt="npx projscan doctor" width="700">
 
 ## Install
 
@@ -94,9 +94,9 @@ npm run test:trust-smoke
 
 The full command catalog is below. Most users should start with the five-command path above instead of scanning the catalog.
 
-<img src="https://raw.githubusercontent.com/abhiyoheswaran1/projscan/v3.7.0/docs/npx%20projscan%20--help.gif" alt="npx projscan --help" width="700">
+<img src="https://raw.githubusercontent.com/abhiyoheswaran1/projscan/v4.0.0/docs/npx%20projscan%20--help.gif" alt="npx projscan --help" width="700">
 
-For a comprehensive walkthrough, see the **[Full Guide](https://github.com/abhiyoheswaran1/projscan/blob/v3.7.0/docs/GUIDE.md)**.
+For a comprehensive walkthrough, see the **[Full Guide](https://github.com/abhiyoheswaran1/projscan/blob/v4.0.0/docs/GUIDE.md)**.
 
 ## Repo Understanding
 
@@ -149,7 +149,6 @@ The report includes file/symbol-backed `claims`, `readFirst` files, entrypoints,
 | `projscan fix` | Auto-fix issues (ESLint, Prettier, Vitest, .editorconfig) |
 | `projscan ci` | CI health gate - SARIF output, `--changed-only` PR-diff mode, exits 1 if score below threshold |
 | `projscan diff` | Compare current health **and hotspot trends** against a baseline |
-| `projscan explain <file>` | Explain a file's purpose, imports, exports, and issues |
 | `projscan diagram` | ASCII architecture diagram of your project |
 | `projscan structure` | Directory tree with file counts |
 | `projscan dependencies` | Dependency analysis - counts, risks, recommendations |
@@ -177,31 +176,25 @@ projscan --help
 <details>
 <summary><strong>projscan structure</strong> - Directory tree with file counts</summary>
 
-<img src="https://raw.githubusercontent.com/abhiyoheswaran1/projscan/v3.7.0/docs/npx%20projscan%20structure.gif" alt="npx projscan structure" width="700">
+<img src="https://raw.githubusercontent.com/abhiyoheswaran1/projscan/v4.0.0/docs/npx%20projscan%20structure.gif" alt="npx projscan structure" width="700">
 </details>
 
 <details>
 <summary><strong>projscan diagram</strong> - Architecture visualization</summary>
 
-<img src="https://raw.githubusercontent.com/abhiyoheswaran1/projscan/v3.7.0/docs/npx%20projscan%20diagram.gif" alt="npx projscan diagram" width="700">
+<img src="https://raw.githubusercontent.com/abhiyoheswaran1/projscan/v4.0.0/docs/npx%20projscan%20diagram.gif" alt="npx projscan diagram" width="700">
 </details>
 
 <details>
 <summary><strong>projscan dependencies</strong> - Dependency analysis</summary>
 
-<img src="https://raw.githubusercontent.com/abhiyoheswaran1/projscan/v3.7.0/docs/npx%20projscan%20dependencies.gif" alt="npx projscan dependencies" width="700">
-</details>
-
-<details>
-<summary><strong>projscan explain</strong> - File explanation</summary>
-
-<img src="https://raw.githubusercontent.com/abhiyoheswaran1/projscan/v3.7.0/docs/npx%20projscan%20explain.gif" alt="npx projscan explain" width="700">
+<img src="https://raw.githubusercontent.com/abhiyoheswaran1/projscan/v4.0.0/docs/npx%20projscan%20dependencies.gif" alt="npx projscan dependencies" width="700">
 </details>
 
 <details>
 <summary><strong>projscan badge</strong> - Health badge generation</summary>
 
-<img src="https://raw.githubusercontent.com/abhiyoheswaran1/projscan/v3.7.0/docs/npx%20projscan%20badge.gif" alt="npx projscan badge" width="700">
+<img src="https://raw.githubusercontent.com/abhiyoheswaran1/projscan/v4.0.0/docs/npx%20projscan%20badge.gif" alt="npx projscan badge" width="700">
 </details>
 
 ### Output Formats
@@ -223,7 +216,7 @@ Run `projscan help` for the generated command-by-command support matrix.
 
 projscan can load local plugins from `.projscan-plugins/` when `PROJSCAN_PLUGINS_PREVIEW=1` is set. The environment flag is kept for explicit local-code opt-in. Analyzer plugins emit normal projscan issues; reporter plugins render supported CLI commands with team-specific output.
 
-**2.0 upgrade notes:** migrating from 1.x or authoring plugins? Start with the [2.0 Migration Guide](https://github.com/abhiyoheswaran1/projscan/blob/v3.7.0/docs/2.0-MIGRATION.md), then use [Plugin Authoring](https://github.com/abhiyoheswaran1/projscan/blob/v3.7.0/docs/PLUGIN-AUTHORING.md), the [Plugin Gallery](https://github.com/abhiyoheswaran1/projscan/blob/v3.7.0/docs/PLUGIN-GALLERY.md), and the [manifest schema](https://github.com/abhiyoheswaran1/projscan/blob/v3.7.0/docs/plugin.schema.json) as the stable contract.
+**2.0 upgrade notes:** migrating from 1.x or authoring plugins? Start with the [2.0 Migration Guide](https://github.com/abhiyoheswaran1/projscan/blob/v4.0.0/docs/2.0-MIGRATION.md), then use [Plugin Authoring](https://github.com/abhiyoheswaran1/projscan/blob/v4.0.0/docs/PLUGIN-AUTHORING.md), the [Plugin Gallery](https://github.com/abhiyoheswaran1/projscan/blob/v4.0.0/docs/PLUGIN-GALLERY.md), and the [manifest schema](https://github.com/abhiyoheswaran1/projscan/blob/v4.0.0/docs/plugin.schema.json) as the stable contract.
 
 ```bash
 projscan plugin list
@@ -234,9 +227,9 @@ PROJSCAN_PLUGINS_PREVIEW=1 projscan doctor --reporter team-radar
 PROJSCAN_PLUGINS_PREVIEW=1 projscan ci --reporter team-radar --min-score 80
 ```
 
-<img src="https://raw.githubusercontent.com/abhiyoheswaran1/projscan/v3.7.0/docs/projscan-reporter-plugin.gif" alt="projscan local reporter plugin rendering a team health report" width="700">
+<img src="https://raw.githubusercontent.com/abhiyoheswaran1/projscan/v4.0.0/docs/projscan-reporter-plugin.gif" alt="projscan local reporter plugin rendering a team health report" width="700">
 
-Reporter plugins are intentionally CLI-only. MCP tools keep returning structured JSON-compatible payloads so agents can reason over stable data, while humans can get a polished local report for their team. Custom presentation, team-branded summaries, and white-label reports belong in reporter plugins rather than new core HTML theming flags. See [Plugin Authoring](https://github.com/abhiyoheswaran1/projscan/blob/v3.7.0/docs/PLUGIN-AUTHORING.md) for manifest shape, `render(context)`, validation, and the trust model.
+Reporter plugins are intentionally CLI-only. MCP tools keep returning structured JSON-compatible payloads so agents can reason over stable data, while humans can get a polished local report for their team. Custom presentation, team-branded summaries, and white-label reports belong in reporter plugins rather than new core HTML theming flags. See [Plugin Authoring](https://github.com/abhiyoheswaran1/projscan/blob/v4.0.0/docs/PLUGIN-AUTHORING.md) for manifest shape, `render(context)`, validation, and the trust model.
 
 ### Options
 
@@ -291,7 +284,7 @@ Python repos now get the same treatment JS/TS has had since 0.6:
 - **Python-aware analyzers.** Missing pytest / ruff / black config. Deprecated packages (nose, simplejson, pycrypto). Unused `pyproject.toml` / `requirements.txt` deps. Missing lockfile.
 - **Code search.** BM25 and semantic modes work on `.py` files out of the box.
 - **Hotspots + dead code.** Same scoring as JS/TS, with `__init__.py` and pytest test-file conventions understood.
-- **MCP tools work unchanged.** `projscan_graph`, `projscan_search`, `projscan_doctor`, `projscan_hotspots`, etc. all accept Python projects. Agents can ask "which files import `pkg.core`?" and get an answer in milliseconds.
+- **MCP tools work unchanged.** `projscan_semantic_graph`, `projscan_search`, `projscan_doctor`, `projscan_hotspots`, etc. all accept Python projects. Agents can ask "which files import `pkg.core`?" and get an answer in milliseconds.
 
 `projscan_upgrade` remains Node-only for now - a Python equivalent (reading pip / poetry metadata) is on the roadmap.
 
@@ -401,7 +394,7 @@ If you read projscan's [Socket report](https://socket.dev/npm/package/projscan),
 ### Audit it yourself
 
 - **Source is open** at [github.com/abhiyoheswaran1/projscan](https://github.com/abhiyoheswaran1/projscan). The npm tarball matches the `dist/` produced by `npm run build` at the matching tag.
-- **Public API surface is locked** by `scripts/check-stability.mjs`, which runs in CI on every PR and fails on any rename or removal of an MCP tool, CLI command, or exit code. See [`docs/STABILITY.md`](https://github.com/abhiyoheswaran1/projscan/blob/v3.7.0/docs/STABILITY.md).
+- **Public API surface is locked** by `scripts/check-stability.mjs`, which runs in CI on every PR and fails on any rename or removal of an MCP tool, CLI command, or exit code. See [`docs/STABILITY.md`](https://github.com/abhiyoheswaran1/projscan/blob/v4.0.0/docs/STABILITY.md).
 - **Run it offline:** `npm install -g projscan` followed by anything except `audit` and `--mode semantic` works without network.
 - **Drop privilege further:** in CI, run projscan in a sandbox that disallows network egress; everything except `audit` will pass.
 
@@ -452,7 +445,7 @@ projscan ci --changed-only                     # Gate only on this PR's diff
 projscan ci --format sarif > projscan.sarif    # SARIF for Code Scanning
 ```
 
-<img src="https://raw.githubusercontent.com/abhiyoheswaran1/projscan/v3.7.0/docs/npx%20projscan%20ci%20--min-score%2070.gif" alt="npx projscan ci --min-score 70" width="700">
+<img src="https://raw.githubusercontent.com/abhiyoheswaran1/projscan/v4.0.0/docs/npx%20projscan%20ci%20--min-score%2070.gif" alt="npx projscan ci --min-score 70" width="700">
 
 ### GitHub Action (recommended)
 
@@ -529,7 +522,7 @@ Fields:
 - `hotspots.limit` / `hotspots.since` - defaults for the `hotspots` command
 - `monorepo.importPolicy` - cross-package import allow/deny rules in monorepos *(0.14+)*
 
-See [`docs/GUIDE.md` → Configuration](https://github.com/abhiyoheswaran1/projscan/blob/v3.7.0/docs/GUIDE.md#configuration-projscanrc) for the full reference (field types, validation behavior, embedding config in `package.json`, monorepo `importPolicy` semantics).
+See [`docs/GUIDE.md` → Configuration](https://github.com/abhiyoheswaran1/projscan/blob/v4.0.0/docs/GUIDE.md#configuration-projscanrc) for the full reference (field types, validation behavior, embedding config in `package.json`, monorepo `importPolicy` semantics).
 
 ## Tracking Health Over Time
 
@@ -542,7 +535,7 @@ projscan diff                       # Compare against baseline
 projscan diff --format markdown     # Markdown diff for PRs
 ```
 
-<img src="https://raw.githubusercontent.com/abhiyoheswaran1/projscan/v3.7.0/docs/npx%20projscan%20diff%20--save-baseline.gif" alt="npx projscan diff --save-baseline" width="700">
+<img src="https://raw.githubusercontent.com/abhiyoheswaran1/projscan/v4.0.0/docs/npx%20projscan%20diff%20--save-baseline.gif" alt="npx projscan diff --save-baseline" width="700">
 
 ## Hotspots - Where to Fix First
 
@@ -631,7 +624,7 @@ Coverage is also automatically joined into `projscan hotspots` when one of those
 
 **This is the primary way to use projscan.** `projscan mcp` starts an [MCP](https://modelcontextprotocol.io) server over stdio so AI coding agents can query your codebase with real structural accuracy - not regex, not grep.
 
-<img src="https://raw.githubusercontent.com/abhiyoheswaran1/projscan/v3.7.0/docs/projscan-agent-demo.gif" alt="projscan answering two agent questions: what breaks if I rename buildCodeGraph (impact analysis with definitions, direct callers, transitive reach), and where should I fix first (ranked hotspots with cyclomatic complexity)" width="700">
+<img src="https://raw.githubusercontent.com/abhiyoheswaran1/projscan/v4.0.0/docs/projscan-agent-demo.gif" alt="projscan answering two agent questions: what breaks if I rename buildCodeGraph (impact analysis with definitions, direct callers, transitive reach), and where should I fix first (ranked hotspots with cyclomatic complexity)" width="700">
 
 Two questions an agent asks; structural answers in milliseconds. *"What breaks if I rename `buildCodeGraph`?"* → 31 direct callers, 97 files reachable. *"Where should I fix first?"* → ranked hotspots with AST cyclomatic complexity, churn, and ownership signals.
 
@@ -653,7 +646,7 @@ command = "npx"
 args = ["-y", "projscan", "mcp"]
 ```
 
-Restart `codex` and the tool surface (`projscan_graph`, `projscan_review`, …) appears alongside Codex's built-ins.
+Restart `codex` and the tool surface (`projscan_semantic_graph`, `projscan_review`, …) appears alongside Codex's built-ins.
 
 ### Gemini CLI (Google)
 
@@ -758,7 +751,7 @@ Capability is advertised under `experimental.fileChanged` on `initialize` so cli
 
 ### What agents can ask
 
-- *"Who imports `src/auth/jwt.ts`?"* → `projscan_graph { file, direction: "importers" }`
+- *"Who imports `src/auth/jwt.ts`?"* → `projscan_semantic_graph { query: { direction: "importers", file: "src/auth/jwt.ts" } }`
 - *"Give me the whole agent-safe graph contract."* → `projscan_semantic_graph`
 - *"Did this wrapper connect a source reader to a dangerous sink?"* → `projscan_dataflow`
 - *"Where is `runAudit` defined?"* → `projscan_search { query: "runAudit", scope: "symbols" }`
@@ -777,13 +770,12 @@ Capability is advertised under `experimental.fileChanged` on `initialize` so cli
 - *"How do I plan the next six product lines?"* → `projscan_release_train`
 - *"How do I wire projscan into this MCP client?"* → `projscan_adoption { action: "mcp_config", client: "codex" }`
 
-### The 47 MCP tools
+### The 45 MCP tools
 
 **Structural (0.6.0 / 0.11 / 0.13 / 0.14 / 0.15 - agent-native):**
 - **`projscan_start`** *(3.0.4)* - first-60-seconds repo orientation. Composes setup diagnostics, `firstTenMinutes`, workflow recipes, workplan, quality scorecard, top risks, adoption gaps, next commands, and optional handoff payload.
 - **`projscan_understand`** *(3.4)* - cited repo-comprehension report with `map`, `flow`, `contracts`, `change`, and `verify` views, read-first files, unknowns, change readiness, verification tiers, and exact next commands.
-- **`projscan_graph`** - query the AST-based code graph. Directions: `imports`, `exports`, `importers`, `symbol_defs`, `package_importers`. Millisecond responses on a warm cache.
-- **`projscan_semantic_graph`** *(3.0)* - stable v3 semantic graph contract with file, function, package, and symbol nodes plus `defines`, `imports`, `imports_package`, `exports`, and `calls` edges.
+- **`projscan_semantic_graph`** *(3.0; query mode 4.0)* - the code graph, two ways. With no `query`: the stable v3 semantic graph contract (file, function, package, and symbol nodes plus `defines`, `imports`, `imports_package`, `exports`, and `calls` edges). With `query: { direction, file?, symbol? }`: one cheap targeted lookup — `imports`, `exports`, `importers`, `symbol_defs`, `package_importers` — with millisecond responses on a warm cache. (Subsumes the former `projscan_graph`, removed in 4.0.)
 - **`projscan_dataflow`** *(3.0)* - focused direct, propagated, and bridge source-to-sink dataflow risks. Next.js and Express request sources are framework-aware, DB/write sinks are receiver-sensitive, and defaults suppress test-file paths, broad readFile/writeFile noise, JavaScript RegExp.exec false positives, and generated-code anxiety; opt into broader scans with `include_tests` / `include_broad_file_io` / `include_generated` or the matching CLI flags.
 - **`projscan_search`** - fast search across `symbols` (exported names), `files` (path substring), or `content` (source substring with line + excerpt). Sub-file mode (`sub_file: true`) embeds per-function for sharper semantic results *(0.15)*.
 - **`projscan_coupling`** *(0.11)* - per-file fan-in / fan-out / instability + circular-import cycles (Tarjan SCC). Filter by `direction: cycles_only | high_fan_in | high_fan_out`.
@@ -811,8 +803,7 @@ Capability is advertised under `experimental.fileChanged` on `initialize` so cli
 - `projscan_analyze` - full project report
 - `projscan_doctor` - health score + issues (now includes `cycle-detected-N` for circular imports as of 0.13)
 - `projscan_hotspots` - risk-ranked files (churn × **AST cyclomatic complexity** × issues × ownership × coverage; falls back to LOC for non-AST languages). Pass `view: "functions"` *(0.13)* for top-N risky individual functions.
-- `projscan_file` - per-file risk + ownership + related issues + CC + fan-in/fan-out + per-function CC table *(0.13)*
-- `projscan_explain` - per-file purpose, imports, exports, smells
+- `projscan_file` - per-file purpose, imports, exports, smells + risk + ownership + related issues + CC + fan-in/fan-out + per-function CC table *(0.13)*
 - `projscan_structure` - directory tree
 - `projscan_coverage` - scariest untested files (coverage × hotspots)
 
@@ -836,7 +827,7 @@ Capability is advertised under `experimental.fileChanged` on `initialize` so cli
 - **`projscan_apply_fix`** *(1.6)* - mechanically execute the safe fix templates. Default is dry-run; pass `confirm: true` to write. Atomic writes, per-apply rollback record at `.projscan-cache/rollbacks/<id>.json`. Reverse with `action: "rollback", rollback_id: ...`. Six templates supported at this release: `unused-dependency-*`, `missing-test-framework`, `missing-eslint`, `missing-prettier`, `missing-editorconfig`, `missing-readme`.
 - **`projscan_taint`** *(1.6)* - source-to-sink reachability over the per-function call graph. Built-in defaults cover common JS / Python sources (`process.env`, `req.body`, etc.) and sinks (`exec`, `eval`, `db.query`, etc.). Project-specific names go in `.projscanrc.json` `taint`. `projscan_review` automatically diffs taint flows between base and head and **blocks any PR that introduces a new flow**. In 3.0.2, review surfaces hardened `newDataflowRisks`, compact `graphEvidence`, and graph-readiness gates for safer handoff.
 
-Analyzer plugins can optionally read graph/dataflow context through `check(rootPath, files, context)` while staying on manifest schema v1. The packaged `graph-context` example shows `context.getSemanticGraph()` and `context.getDataflow()` in a real analyzer. For analyzer and reporter plugin authoring, manifest validation, `--reporter <name>`, and the trust model, see [Plugin Authoring](https://github.com/abhiyoheswaran1/projscan/blob/v3.7.0/docs/PLUGIN-AUTHORING.md).
+Analyzer plugins can optionally read graph/dataflow context through `check(rootPath, files, context)` while staying on manifest schema v1. The packaged `graph-context` example shows `context.getSemanticGraph()` and `context.getDataflow()` in a real analyzer. For analyzer and reporter plugin authoring, manifest validation, `--reporter <name>`, and the trust model, see [Plugin Authoring](https://github.com/abhiyoheswaran1/projscan/blob/v4.0.0/docs/PLUGIN-AUTHORING.md).
 
 ### Context-window budgeting
 

package/dist/cli/index.js

@@ -6,7 +6,6 @@ import { registerCi } from './commands/ci.js';
 import { registerDiff } from './commands/diff.js';
 import { registerFix } from './commands/fix.js';
 import { registerFile } from './commands/file.js';
-import { registerExplain } from './commands/explain.js';
 import { registerDiagram } from './commands/diagram.js';
 import { registerStructure } from './commands/structure.js';
 import { registerDependencies } from './commands/dependencies.js';
@@ -64,7 +63,6 @@ registerCi();
 registerDiff();
 registerFix();
 registerFile();
-registerExplain();
 registerDiagram();
 registerStructure();
 registerDependencies();

package/dist/cli/index.js.map

@@ -1 +1 @@
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package/dist/core/deprecations.d.ts

@@ -0,0 +1,30 @@
+/**
+ * Tool/command deprecation primitives (3.8 deprecation pass).
+ *
+ * projscan ships a 1.0 stability contract: tools and CLI commands are not
+ * removed or renamed within a major. The 4.0 surface consolidation removes a
+ * long tail of tools, so 3.8 introduces a *deprecation* signal first — a
+ * non-breaking, reversible marker that tells agents and humans "this still
+ * works today, but is going away; here is the replacement". Removal happens in
+ * {@link REMOVAL_VERSION}, never before.
+ *
+ * This module is the single source of truth for how a deprecation renders, so
+ * the MCP tool surface (description prefix) and the CLI (stderr notice) stay
+ * in lockstep. See docs/MIGRATION-4.0.md.
+ */
+import type { ToolDeprecation } from '../types.js';
+export type { ToolDeprecation };
+/** The major release in which deprecated tools/commands are actually removed. */
+export declare const REMOVAL_VERSION = "4.0";
+/**
+ * Prefix prepended to a deprecated MCP tool's description. Machine-greppable
+ * (`[DEPRECATED`) and human-readable, with a trailing space so it composes
+ * cleanly in front of the existing description.
+ */
+export declare function deprecationDescriptionPrefix(dep: ToolDeprecation): string;
+/**
+ * One-line stderr notice for a deprecated CLI command. `command` is the bare
+ * subcommand name (e.g. "explain"); `replacedBy` should read as the
+ * replacement invocation (e.g. "projscan file").
+ */
+export declare function formatCliDeprecationNotice(command: string, dep: ToolDeprecation): string;

package/dist/core/deprecations.js

@@ -0,0 +1,34 @@
+/**
+ * Tool/command deprecation primitives (3.8 deprecation pass).
+ *
+ * projscan ships a 1.0 stability contract: tools and CLI commands are not
+ * removed or renamed within a major. The 4.0 surface consolidation removes a
+ * long tail of tools, so 3.8 introduces a *deprecation* signal first — a
+ * non-breaking, reversible marker that tells agents and humans "this still
+ * works today, but is going away; here is the replacement". Removal happens in
+ * {@link REMOVAL_VERSION}, never before.
+ *
+ * This module is the single source of truth for how a deprecation renders, so
+ * the MCP tool surface (description prefix) and the CLI (stderr notice) stay
+ * in lockstep. See docs/MIGRATION-4.0.md.
+ */
+/** The major release in which deprecated tools/commands are actually removed. */
+export const REMOVAL_VERSION = '4.0';
+/**
+ * Prefix prepended to a deprecated MCP tool's description. Machine-greppable
+ * (`[DEPRECATED`) and human-readable, with a trailing space so it composes
+ * cleanly in front of the existing description.
+ */
+export function deprecationDescriptionPrefix(dep) {
+    return `[DEPRECATED since ${dep.since}, removed in ${REMOVAL_VERSION} — use ${dep.replacedBy}] `;
+}
+/**
+ * One-line stderr notice for a deprecated CLI command. `command` is the bare
+ * subcommand name (e.g. "explain"); `replacedBy` should read as the
+ * replacement invocation (e.g. "projscan file").
+ */
+export function formatCliDeprecationNotice(command, dep) {
+    const base = `projscan ${command} is deprecated (since ${dep.since}) and will be removed in ${REMOVAL_VERSION} — use ${dep.replacedBy} instead.`;
+    return dep.note ? `${base} ${dep.note}` : base;
+}
+//# sourceMappingURL=deprecations.js.map

package/dist/core/deprecations.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"deprecations.js","sourceRoot":"","sources":["../../src/core/deprecations.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;GAaG;AAMH,iFAAiF;AACjF,MAAM,CAAC,MAAM,eAAe,GAAG,KAAK,CAAC;AAErC;;;;GAIG;AACH,MAAM,UAAU,4BAA4B,CAAC,GAAoB;IAC/D,OAAO,qBAAqB,GAAG,CAAC,KAAK,gBAAgB,eAAe,UAAU,GAAG,CAAC,UAAU,IAAI,CAAC;AACnG,CAAC;AAED;;;;GAIG;AACH,MAAM,UAAU,0BAA0B,CAAC,OAAe,EAAE,GAAoB;IAC9E,MAAM,IAAI,GAAG,YAAY,OAAO,yBAAyB,GAAG,CAAC,KAAK,4BAA4B,eAAe,UAAU,GAAG,CAAC,UAAU,WAAW,CAAC;IACjJ,OAAO,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,GAAG,IAAI,IAAI,GAAG,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC;AACjD,CAAC"}

package/dist/core/fixSuggest.js

@@ -86,7 +86,7 @@ const TEMPLATES = [
             why: 'High dependency counts compound supply-chain risk and slow installs. Beyond ~50 prod deps, projects rarely need every one - some are dead, some are duplicates, some have native replacements.',
             where: [{ file: 'package.json' }],
             instruction: 'Run `projscan_dependencies` to see the full list, then `projscan_outdated` and `projscan_audit` for surface area. ' +
-                'For each dep that looks suspicious, run `projscan_graph { direction: "package_importers", target: "<name>" }` to see what (if anything) actually uses it. ' +
+                'For each dep that looks suspicious, run `projscan_semantic_graph { query: { direction: "package_importers", symbol: "<name>" } }` to see what (if anything) actually uses it. ' +
                 'Drop the ones with zero importers; consider native replacements for shimming-shaped deps (e.g. `lodash/get` → optional chaining).',
         }),
     },
@@ -102,7 +102,7 @@ const TEMPLATES = [
                 headline: i.title,
                 why: i.description,
                 where: i.locations ?? [{ file: 'package.json' }],
-                instruction: `Audit "${name}": call \`projscan_graph { direction: "package_importers", target: "${name}" }\` to see who imports it. ` +
+                instruction: `Audit "${name}": call \`projscan_semantic_graph { query: { direction: "package_importers", symbol: "${name}" } }\` to see who imports it. ` +
                     `If it can be replaced with a lighter/native alternative, plan that migration; if it must stay, pin to an exact version (drop the \`^\` / \`>=\`) and document the choice.`,
             };
         },
@@ -151,7 +151,7 @@ const TEMPLATES = [
             headline: i.title,
             why: 'Catch-all directories (utils/helpers/lib/shared) are the project graveyard. Every file under one is implicitly "miscellaneous", which means changes touching it also rarely have a clear owner.',
             where: i.locations ?? [],
-            instruction: 'Group the files under the flagged directory by domain (e.g. `auth/`, `format/`, `validation/`) using `projscan_graph` to see which symbols are imported together. ' +
+            instruction: 'Group the files under the flagged directory by domain (e.g. `auth/`, `format/`, `validation/`) using `projscan_semantic_graph` to see which symbols are imported together. ' +
                 'Move them into domain-named subdirectories. Update imports - your editor\'s rename-and-update should handle the bulk; finish with a `projscan analyze` to verify no leftover imports broke.',
         }),
     },
@@ -165,7 +165,7 @@ const TEMPLATES = [
             why: "An export with zero importers either (a) was orphaned by a refactor and is genuinely dead, or (b) is part of the project's public API and projscan can't see who consumes it. " +
                 'Either case deserves resolution: cleanup or an explicit "public" annotation.',
             where: i.locations ?? [],
-            instruction: 'For each flagged file: confirm with `projscan_graph { direction: "importers", target: "<file>" }`. ' +
+            instruction: 'For each flagged file: confirm with `projscan_semantic_graph { query: { direction: "importers", file: "<file>" } }`. ' +
                 'If the result is genuinely empty AND this isn\'t package.json#main / #exports, delete the file (or just the unused exports). ' +
                 'If it IS public surface (entry point, re-exported), add it to package.json#exports or list the file in .projscanrc `disableRules: ["dead-code"]`.',
         }),
@@ -497,7 +497,7 @@ function staticHeadlineFor(issue) {
     if (issue.id.startsWith('large-') && issue.id.endsWith('-dir'))
         return 'Split the directory by domain.';
     if (issue.id === 'dead-code' || issue.id.startsWith('dead-code-'))
-        return 'Confirm with `projscan_graph importers` then delete or expose.';
+        return 'Confirm with `projscan_semantic_graph { query: { direction: "importers", file: "<file>" } }` then delete or expose.';
     if (issue.id === 'missing-test-framework' || issue.id === 'missing-python-test-framework')
         return issue.id.includes('python') ? 'Install pytest + write one smoke test.' : 'Install vitest + write one smoke test.';
     if (issue.id === 'no-test-files' || issue.id === 'no-python-test-files')

package/dist/core/fixSuggest.js.map

@@ -1 +1 @@
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package/dist/core/graphQuery.d.ts

@@ -0,0 +1,23 @@
+/**
+ * Targeted code-graph queries (4.0 consolidation).
+ *
+ * Extracted from the (removed) `projscan_graph` tool so the capability lives in
+ * one tested place and folds into `projscan_semantic_graph` — which previously
+ * only dumped the whole graph. This is what makes semantic_graph a true
+ * superset of the old graph tool: it answers the same targeted "who imports X",
+ * "what does X export", "where is symbol S defined" questions without serializing
+ * the entire graph.
+ */
+import { type CodeGraph } from './codeGraph.js';
+export type GraphQueryDirection = 'imports' | 'exports' | 'importers' | 'symbol_defs' | 'package_importers';
+export interface GraphQueryInput {
+    direction: GraphQueryDirection;
+    /** Repo-relative file path (for imports/exports/importers). */
+    file?: string;
+    /** Symbol or package name (for symbol_defs/package_importers). */
+    symbol?: string;
+    /** Max entries returned (1–500, default 50). */
+    limit?: number;
+}
+/** Run one targeted query against a built code graph. Throws on missing args. */
+export declare function runGraphQuery(graph: CodeGraph, input: GraphQueryInput): Record<string, unknown>;

package/dist/core/graphQuery.js

@@ -0,0 +1,48 @@
+/**
+ * Targeted code-graph queries (4.0 consolidation).
+ *
+ * Extracted from the (removed) `projscan_graph` tool so the capability lives in
+ * one tested place and folds into `projscan_semantic_graph` — which previously
+ * only dumped the whole graph. This is what makes semantic_graph a true
+ * superset of the old graph tool: it answers the same targeted "who imports X",
+ * "what does X export", "where is symbol S defined" questions without serializing
+ * the entire graph.
+ */
+import { filesImportingFile, filesImportingPackage, filesDefiningSymbol, exportsOf, importsOf, } from './codeGraph.js';
+const DEFAULT_LIMIT = 50;
+/** Run one targeted query against a built code graph. Throws on missing args. */
+export function runGraphQuery(graph, input) {
+    const { direction, file, symbol } = input;
+    const limit = Math.max(1, Math.min(500, typeof input.limit === 'number' ? input.limit : DEFAULT_LIMIT));
+    switch (direction) {
+        case 'imports': {
+            if (!file)
+                throw new Error('direction=imports requires a `file` argument (repo-relative path, e.g. "src/auth.ts").');
+            return { file, imports: importsOf(graph, file).slice(0, limit) };
+        }
+        case 'exports': {
+            if (!file)
+                throw new Error('direction=exports requires a `file` argument (repo-relative path).');
+            return { file, exports: exportsOf(graph, file).slice(0, limit) };
+        }
+        case 'importers': {
+            if (!file)
+                throw new Error('direction=importers requires a `file` argument (repo-relative path).');
+            return { file, importers: filesImportingFile(graph, file).slice(0, limit) };
+        }
+        case 'symbol_defs': {
+            if (!symbol)
+                throw new Error('direction=symbol_defs requires a `symbol` argument (the exported name, e.g. "authenticate").');
+            return { symbol, definedIn: filesDefiningSymbol(graph, symbol).slice(0, limit) };
+        }
+        case 'package_importers': {
+            const pkg = symbol ?? file;
+            if (!pkg)
+                throw new Error('direction=package_importers requires a `symbol` (or `file`) arg (the npm package name, e.g. "chalk").');
+            return { package: pkg, importers: filesImportingPackage(graph, pkg).slice(0, limit) };
+        }
+        default:
+            throw new Error(`unknown direction "${String(direction)}". Valid: imports, exports, importers, symbol_defs, package_importers.`);
+    }
+}
+//# sourceMappingURL=graphQuery.js.map

package/dist/core/graphQuery.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"graphQuery.js","sourceRoot":"","sources":["../../src/core/graphQuery.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAEH,OAAO,EACL,kBAAkB,EAClB,qBAAqB,EACrB,mBAAmB,EACnB,SAAS,EACT,SAAS,GAEV,MAAM,gBAAgB,CAAC;AAmBxB,MAAM,aAAa,GAAG,EAAE,CAAC;AAEzB,iFAAiF;AACjF,MAAM,UAAU,aAAa,CAAC,KAAgB,EAAE,KAAsB;IACpE,MAAM,EAAE,SAAS,EAAE,IAAI,EAAE,MAAM,EAAE,GAAG,KAAK,CAAC;IAC1C,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,IAAI,CAAC,GAAG,CAAC,GAAG,EAAE,OAAO,KAAK,CAAC,KAAK,KAAK,QAAQ,CAAC,CAAC,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,aAAa,CAAC,CAAC,CAAC;IAExG,QAAQ,SAAS,EAAE,CAAC;QAClB,KAAK,SAAS,CAAC,CAAC,CAAC;YACf,IAAI,CAAC,IAAI;gBAAE,MAAM,IAAI,KAAK,CAAC,wFAAwF,CAAC,CAAC;YACrH,OAAO,EAAE,IAAI,EAAE,OAAO,EAAE,SAAS,CAAC,KAAK,EAAE,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,EAAE,KAAK,CAAC,EAAE,CAAC;QACnE,CAAC;QACD,KAAK,SAAS,CAAC,CAAC,CAAC;YACf,IAAI,CAAC,IAAI;gBAAE,MAAM,IAAI,KAAK,CAAC,oEAAoE,CAAC,CAAC;YACjG,OAAO,EAAE,IAAI,EAAE,OAAO,EAAE,SAAS,CAAC,KAAK,EAAE,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,EAAE,KAAK,CAAC,EAAE,CAAC;QACnE,CAAC;QACD,KAAK,WAAW,CAAC,CAAC,CAAC;YACjB,IAAI,CAAC,IAAI;gBAAE,MAAM,IAAI,KAAK,CAAC,sEAAsE,CAAC,CAAC;YACnG,OAAO,EAAE,IAAI,EAAE,SAAS,EAAE,kBAAkB,CAAC,KAAK,EAAE,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,EAAE,KAAK,CAAC,EAAE,CAAC;QAC9E,CAAC;QACD,KAAK,aAAa,CAAC,CAAC,CAAC;YACnB,IAAI,CAAC,MAAM;gBAAE,MAAM,IAAI,KAAK,CAAC,8FAA8F,CAAC,CAAC;YAC7H,OAAO,EAAE,MAAM,EAAE,SAAS,EAAE,mBAAmB,CAAC,KAAK,EAAE,MAAM,CAAC,CAAC,KAAK,CAAC,CAAC,EAAE,KAAK,CAAC,EAAE,CAAC;QACnF,CAAC;QACD,KAAK,mBAAmB,CAAC,CAAC,CAAC;YACzB,MAAM,GAAG,GAAG,MAAM,IAAI,IAAI,CAAC;YAC3B,IAAI,CAAC,GAAG;gBAAE,MAAM,IAAI,KAAK,CAAC,uGAAuG,CAAC,CAAC;YACnI,OAAO,EAAE,OAAO,EAAE,GAAG,EAAE,SAAS,EAAE,qBAAqB,CAAC,KAAK,EAAE,GAAG,CAAC,CAAC,KAAK,CAAC,CAAC,EAAE,KAAK,CAAC,EAAE,CAAC;QACxF,CAAC;QACD;YACE,MAAM,IAAI,KAAK,CAAC,sBAAsB,MAAM,CAAC,SAAS,CAAC,wEAAwE,CAAC,CAAC;IACrI,CAAC;AACH,CAAC"}

package/dist/mcp/tools/costSummary.js

@@ -347,12 +347,10 @@ const STATIC_EXPECTED_TOKENS = {
     projscan_audit: 1500,
     projscan_upgrade: 1000,
     projscan_search: 2500,
-    projscan_graph: 4500,
     projscan_semantic_graph: 6000,
     projscan_dataflow: 3500,
     projscan_structure: 3000,
     projscan_analyze: 3500,
-    projscan_explain: 1500,
     projscan_explain_issue: 800,
     projscan_fix_suggest: 800,
     projscan_apply_fix: 1500,

package/dist/mcp/tools/costSummary.js.map

@@ -1 +1 @@
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package/dist/mcp/tools/semanticGraph.js

@@ -1,20 +1,36 @@
 import { scanRepository } from '../../core/repositoryScanner.js';
 import { buildCodeGraph } from '../../core/codeGraph.js';
 import { buildSemanticGraph } from '../../core/semanticGraph.js';
+import { runGraphQuery } from '../../core/graphQuery.js';
 import { loadCachedGraph, saveCachedGraph } from '../../core/indexCache.js';
 export const semanticGraphTool = {
     name: 'projscan_semantic_graph',
-    description: 'Return the stable v3 semantic graph: file/function/package/symbol nodes plus imports, exports, defines, and calls edges. Use when an agent needs one normalized graph contract instead of several targeted graph queries.',
+    description: 'The code graph, two ways. With no `query`: returns the stable v3 semantic graph (file/function/package/symbol nodes plus imports, exports, defines, and calls edges). With `query`: answers one cheap, targeted question instead of serializing the whole graph — who imports a file, what a file imports/exports, where a symbol is defined, or which files import a package. (The targeted mode subsumes the former projscan_graph tool, removed in 4.0.)',
     inputSchema: {
         type: 'object',
         properties: {
+            query: {
+                type: 'object',
+                description: 'Optional. Ask one targeted question instead of returning the whole graph.',
+                properties: {
+                    direction: {
+                        type: 'string',
+                        enum: ['imports', 'exports', 'importers', 'symbol_defs', 'package_importers'],
+                        description: '"imports" (what the file imports), "exports" (what the file exports), "importers" (who imports the file), "symbol_defs" (files defining the symbol), "package_importers" (files importing a package by name).',
+                    },
+                    file: { type: 'string', description: 'Repo-relative file path (for imports/exports/importers).' },
+                    symbol: { type: 'string', description: 'Symbol or package name (for symbol_defs/package_importers).' },
+                    limit: { type: 'number', description: 'Max entries returned (default 50, max 500).' },
+                },
+                required: ['direction'],
+            },
             max_nodes: {
                 type: 'number',
-                description: 'Maximum graph nodes to return. Default 10000.',
+                description: 'Full-graph mode only. Maximum graph nodes to return. Default 10000.',
             },
             max_edges: {
                 type: 'number',
-                description: 'Maximum graph edges to return. Default 25000.',
+                description: 'Full-graph mode only. Maximum graph edges to return. Default 25000.',
             },
             max_tokens: {
                 type: 'number',
@@ -27,6 +43,15 @@ export const semanticGraphTool = {
         const cached = await loadCachedGraph(rootPath);
         const graph = await buildCodeGraph(rootPath, scan.files, cached);
         await saveCachedGraph(rootPath, graph);
+        const query = args.query;
+        if (query && typeof query.direction === 'string') {
+            return runGraphQuery(graph, {
+                direction: query.direction,
+                file: typeof query.file === 'string' ? query.file : undefined,
+                symbol: typeof query.symbol === 'string' ? query.symbol : undefined,
+                limit: typeof query.limit === 'number' ? query.limit : undefined,
+            });
+        }
         return buildSemanticGraph(graph, {
             maxNodes: typeof args.max_nodes === 'number' && Number.isFinite(args.max_nodes)
                 ? args.max_nodes

package/dist/mcp/tools/semanticGraph.js.map

@@ -1 +1 @@
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package/dist/mcp/tools.js

@@ -11,7 +11,6 @@
 import { analyzeTool } from './tools/analyze.js';
 import { doctorTool } from './tools/doctor.js';
 import { hotspotsTool } from './tools/hotspots.js';
-import { explainTool } from './tools/explain.js';
 import { fileTool } from './tools/file.js';
 import { structureTool } from './tools/structure.js';
 import { dependenciesTool } from './tools/dependencies.js';
@@ -19,7 +18,6 @@ import { outdatedTool } from './tools/outdated.js';
 import { auditTool } from './tools/audit.js';
 import { upgradeTool } from './tools/upgrade.js';
 import { coverageTool } from './tools/coverage.js';
-import { graphTool } from './tools/graph.js';
 import { semanticGraphTool } from './tools/semanticGraph.js';
 import { couplingTool } from './tools/coupling.js';
 import { workspacesTool } from './tools/workspaces.js';
@@ -55,11 +53,11 @@ import { qualityScorecardTool } from './tools/qualityScorecard.js';
 import { adoptionTool } from './tools/adoption.js';
 import { startTool } from './tools/start.js';
 import { understandTool } from './tools/understand.js';
+import { deprecationDescriptionPrefix } from '../core/deprecations.js';
 const tools = [
     analyzeTool,
     doctorTool,
     hotspotsTool,
-    explainTool,
     fileTool,
     structureTool,
     dependenciesTool,
@@ -67,7 +65,6 @@ const tools = [
     auditTool,
     upgradeTool,
     coverageTool,
-    graphTool,
     semanticGraphTool,
     couplingTool,
     workspacesTool,
@@ -105,7 +102,16 @@ const tools = [
     coordinateWatchTool,
 ];
 export function getToolDefinitions() {
-    return tools.map(({ name, description, inputSchema }) => ({ name, description, inputSchema }));
+    return tools.map(({ name, description, inputSchema, deprecated }) => {
+        const def = {
+            name,
+            description: deprecated ? deprecationDescriptionPrefix(deprecated) + description : description,
+            inputSchema,
+        };
+        if (deprecated)
+            def.deprecated = deprecated;
+        return def;
+    });
 }
 export function getToolHandler(name) {
     return tools.find((t) => t.name === name)?.handler;

package/dist/mcp/tools.js.map

@@ -1 +1 @@
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+{"version":3,"file":"tools.js","sourceRoot":"","sources":["../../src/mcp/tools.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAEH,OAAO,EAAE,WAAW,EAAE,MAAM,oBAAoB,CAAC;AACjD,OAAO,EAAE,UAAU,EAAE,MAAM,mBAAmB,CAAC;AAC/C,OAAO,EAAE,YAAY,EAAE,MAAM,qBAAqB,CAAC;AACnD,OAAO,EAAE,QAAQ,EAAE,MAAM,iBAAiB,CAAC;AAC3C,OAAO,EAAE,aAAa,EAAE,MAAM,sBAAsB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAC;AAC3D,OAAO,EAAE,YAAY,EAAE,MAAM,qBAAqB,CAAC;AACnD,OAAO,EAAE,SAAS,EAAE,MAAM,kBAAkB,CAAC;AAC7C,OAAO,EAAE,WAAW,EAAE,MAAM,oBAAoB,CAAC;AACjD,OAAO,EAAE,YAAY,EAAE,MAAM,qBAAqB,CAAC;AACnD,OAAO,EAAE,iBAAiB,EAAE,MAAM,0BAA0B,CAAC;AAC7D,OAAO,EAAE,YAAY,EAAE,MAAM,qBAAqB,CAAC;AACnD,OAAO,EAAE,cAAc,EAAE,MAAM,uBAAuB,CAAC;AACvD,OAAO,EAAE,UAAU,EAAE,MAAM,mBAAmB,CAAC;AAC/C,OAAO,EAAE,UAAU,EAAE,MAAM,mBAAmB,CAAC;AAC/C,OAAO,EAAE,cAAc,EAAE,MAAM,uBAAuB,CAAC;AACvD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAC;AAC3D,OAAO,EAAE,UAAU,EAAE,MAAM,mBAAmB,CAAC;AAC/C,OAAO,EAAE,aAAa,EAAE,MAAM,sBAAsB,CAAC;AACrD,OAAO,EAAE,SAAS,EAAE,MAAM,kBAAkB,CAAC;AAC7C,OAAO,EAAE,aAAa,EAAE,MAAM,sBAAsB,CAAC;AACrD,OAAO,EAAE,SAAS,EAAE,MAAM,kBAAkB,CAAC;AAC7C,OAAO,EAAE,cAAc,EAAE,MAAM,uBAAuB,CAAC;AACvD,OAAO,EAAE,mBAAmB,EAAE,MAAM,4BAA4B,CAAC;AACjE,OAAO,EAAE,UAAU,EAAE,MAAM,mBAAmB,CAAC;AAC/C,OAAO,EAAE,WAAW,EAAE,MAAM,oBAAoB,CAAC;AACjD,OAAO,EAAE,UAAU,EAAE,MAAM,mBAAmB,CAAC;AAC/C,OAAO,EAAE,kBAAkB,EAAE,MAAM,2BAA2B,CAAC;AAC/D,OAAO,EAAE,YAAY,EAAE,MAAM,qBAAqB,CAAC;AACnD,OAAO,EAAE,SAAS,EAAE,MAAM,kBAAkB,CAAC;AAC7C,OAAO,EAAE,YAAY,EAAE,MAAM,qBAAqB,CAAC;AACnD,OAAO,EAAE,eAAe,EAAE,MAAM,wBAAwB,CAAC;AACzD,OAAO,EAAE,eAAe,EAAE,MAAM,wBAAwB,CAAC;AACzD,OAAO,EAAE,UAAU,EAAE,MAAM,mBAAmB,CAAC;AAC/C,OAAO,EAAE,aAAa,EAAE,MAAM,sBAAsB,CAAC;AACrD,OAAO,EAAE,YAAY,EAAE,MAAM,qBAAqB,CAAC;AACnD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAC;AAC3D,OAAO,EAAE,WAAW,EAAE,MAAM,oBAAoB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAC;AAC3D,OAAO,EAAE,kBAAkB,EAAE,MAAM,2BAA2B,CAAC;AAC/D,OAAO,EAAE,cAAc,EAAE,MAAM,uBAAuB,CAAC;AACvD,OAAO,EAAE,oBAAoB,EAAE,MAAM,6BAA6B,CAAC;AACnE,OAAO,EAAE,YAAY,EAAE,MAAM,qBAAqB,CAAC;AACnD,OAAO,EAAE,SAAS,EAAE,MAAM,kBAAkB,CAAC;AAC7C,OAAO,EAAE,cAAc,EAAE,MAAM,uBAAuB,CAAC;AACvD,OAAO,EAAE,4BAA4B,EAAE,MAAM,yBAAyB,CAAC;AAMvE,MAAM,KAAK,GAAc;IACvB,WAAW;IACX,UAAU;IACV,YAAY;IACZ,QAAQ;IACR,aAAa;IACb,gBAAgB;IAChB,YAAY;IACZ,SAAS;IACT,WAAW;IACX,YAAY;IACZ,iBAAiB;IACjB,YAAY;IACZ,cAAc;IACd,UAAU;IACV,UAAU;IACV,cAAc;IACd,gBAAgB;IAChB,UAAU;IACV,UAAU;IACV,WAAW;IACX,UAAU;IACV,kBAAkB;IAClB,YAAY;IACZ,SAAS;IACT,YAAY;IACZ,eAAe;IACf,eAAe;IACf,UAAU;IACV,aAAa;IACb,YAAY;IACZ,gBAAgB;IAChB,WAAW;IACX,gBAAgB;IAChB,kBAAkB;IAClB,cAAc;IACd,oBAAoB;IACpB,YAAY;IACZ,SAAS;IACT,cAAc;IACd,aAAa;IACb,SAAS;IACT,aAAa;IACb,SAAS;IACT,cAAc;IACd,mBAAmB;CACpB,CAAC;AAEF,MAAM,UAAU,kBAAkB;IAChC,OAAO,KAAK,CAAC,GAAG,CAAC,CAAC,EAAE,IAAI,EAAE,WAAW,EAAE,WAAW,EAAE,UAAU,EAAE,EAAE,EAAE;QAClE,MAAM,GAAG,GAAsB;YAC7B,IAAI;YACJ,WAAW,EAAE,UAAU,CAAC,CAAC,CAAC,4BAA4B,CAAC,UAAU,CAAC,GAAG,WAAW,CAAC,CAAC,CAAC,WAAW;YAC9F,WAAW;SACZ,CAAC;QACF,IAAI,UAAU;YAAE,GAAG,CAAC,UAAU,GAAG,UAAU,CAAC;QAC5C,OAAO,GAAG,CAAC;IACb,CAAC,CAAC,CAAC;AACL,CAAC;AAED,MAAM,UAAU,cAAc,CAAC,IAAY;IACzC,OAAO,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,KAAK,IAAI,CAAC,EAAE,OAAO,CAAC;AACrD,CAAC"}

package/dist/projscan-sbom.cdx.json

@@ -1,23 +1,23 @@
 {
   "bomFormat": "CycloneDX",
   "specVersion": "1.5",
-  "serialNumber": "urn:uuid:6dab452f-f2df-4c0a-b793-e7ba294a3df5",
+  "serialNumber": "urn:uuid:89f8c0f1-482c-4e76-b7b6-64830539ffdc",
   "version": 1,
   "metadata": {
-    "timestamp": "2026-06-05T15:33:32.104Z",
+    "timestamp": "2026-06-05T19:19:59.691Z",
     "tools": [
       {
         "vendor": "projscan",
         "name": "projscan-sbom-generator",
-        "version": "3.7.0"
+        "version": "4.0.0"
       }
     ],
     "component": {
       "type": "application",
-      "bom-ref": "pkg:npm/projscan@3.7.0",
+      "bom-ref": "pkg:npm/projscan@4.0.0",
       "name": "projscan",
-      "version": "3.7.0",
-      "purl": "pkg:npm/projscan@3.7.0"
+      "version": "4.0.0",
+      "purl": "pkg:npm/projscan@4.0.0"
     }
   },
   "components": [

package/dist/tool-manifest.json

@@ -1,9 +1,9 @@
 {
   "name": "projscan",
-  "version": "3.7.0",
+  "version": "4.0.0",
   "mcpProtocolVersion": "2025-03-26",
-  "generatedAt": "2026-06-05T15:33:37.612Z",
-  "toolCount": 47,
+  "generatedAt": "2026-06-05T19:20:05.305Z",
+  "toolCount": 45,
   "tools": [
     {
       "name": "projscan_analyze",
@@ -76,22 +76,6 @@
         }
       }
     },
-    {
-      "name": "projscan_explain",
-      "description": "Explain a single file: purpose, imports, exports, and potential issues. Useful for understanding unfamiliar code before editing.",
-      "inputSchema": {
-        "type": "object",
-        "properties": {
-          "file": {
-            "type": "string",
-            "description": "Path to the file relative to the project root."
-          }
-        },
-        "required": [
-          "file"
-        ]
-      }
-    },
     {
       "name": "projscan_file",
       "description": "Drill into a single file: purpose, imports, exports, churn/risk/ownership, related health issues, AST cyclomatic complexity, coupling (fan-in / fan-out), and per-function CC ranked by complexity. Use this after projscan_hotspots when deciding how to approach a specific risky file.",
@@ -226,57 +210,50 @@
       }
     },
     {
-      "name": "projscan_graph",
-      "description": "Query the AST-based code graph directly. Returns imports, exports, importers, or symbol definitions for a file or symbol. Agents should prefer this over analyze/doctor/explain for targeted structural questions - it is much cheaper and more accurate.",
+      "name": "projscan_semantic_graph",
+      "description": "The code graph, two ways. With no `query`: returns the stable v3 semantic graph (file/function/package/symbol nodes plus imports, exports, defines, and calls edges). With `query`: answers one cheap, targeted question instead of serializing the whole graph — who imports a file, what a file imports/exports, where a symbol is defined, or which files import a package. (The targeted mode subsumes the former projscan_graph tool, removed in 4.0.)",
       "inputSchema": {
         "type": "object",
         "properties": {
-          "file": {
-            "type": "string",
-            "description": "File path (relative to project root) to query."
-          },
-          "symbol": {
-            "type": "string",
-            "description": "Symbol name to query (e.g. a function or class). Use instead of `file` to find where a symbol is defined."
-          },
-          "direction": {
-            "type": "string",
-            "description": "What to return: \"imports\" (what the file imports), \"exports\" (what the file exports), \"importers\" (who imports the file), \"symbol_defs\" (files defining the symbol), \"package_importers\" (files importing a package by name).",
-            "enum": [
-              "imports",
-              "exports",
-              "importers",
-              "symbol_defs",
-              "package_importers"
+          "query": {
+            "type": "object",
+            "description": "Optional. Ask one targeted question instead of returning the whole graph.",
+            "properties": {
+              "direction": {
+                "type": "string",
+                "enum": [
+                  "imports",
+                  "exports",
+                  "importers",
+                  "symbol_defs",
+                  "package_importers"
+                ],
+                "description": "\"imports\" (what the file imports), \"exports\" (what the file exports), \"importers\" (who imports the file), \"symbol_defs\" (files defining the symbol), \"package_importers\" (files importing a package by name)."
+              },
+              "file": {
+                "type": "string",
+                "description": "Repo-relative file path (for imports/exports/importers)."
+              },
+              "symbol": {
+                "type": "string",
+                "description": "Symbol or package name (for symbol_defs/package_importers)."
+              },
+              "limit": {
+                "type": "number",
+                "description": "Max entries returned (default 50, max 500)."
+              }
+            },
+            "required": [
+              "direction"
             ]
           },
-          "limit": {
-            "type": "number",
-            "description": "Max entries returned (default 50)."
-          },
-          "max_tokens": {
-            "type": "number",
-            "description": "Cap the response to roughly this many tokens."
-          }
-        },
-        "required": [
-          "direction"
-        ]
-      }
-    },
-    {
-      "name": "projscan_semantic_graph",
-      "description": "Return the stable v3 semantic graph: file/function/package/symbol nodes plus imports, exports, defines, and calls edges. Use when an agent needs one normalized graph contract instead of several targeted graph queries.",
-      "inputSchema": {
-        "type": "object",
-        "properties": {
           "max_nodes": {
             "type": "number",
-            "description": "Maximum graph nodes to return. Default 10000."
+            "description": "Full-graph mode only. Maximum graph nodes to return. Default 10000."
           },
           "max_edges": {
             "type": "number",
-            "description": "Maximum graph edges to return. Default 25000."
+            "description": "Full-graph mode only. Maximum graph edges to return. Default 25000."
           },
           "max_tokens": {
             "type": "number",

package/dist/types.d.ts

@@ -1941,6 +1941,18 @@ export interface FunctionDetail {
      */
     fanIn?: number;
 }
+/**
+ * A reversible deprecation marker (3.8 deprecation pass). Present on a tool
+ * means "still works, but slated for removal in 4.0 — prefer `replacedBy`".
+ */
+export interface ToolDeprecation {
+    /** Version the deprecation was announced in (e.g. "3.8.0"). */
+    since: string;
+    /** The recommended replacement (tool name for MCP, invocation for CLI). */
+    replacedBy: string;
+    /** Optional one-line rationale shown to humans/agents. */
+    note?: string;
+}
 export interface McpToolDefinition {
     name: string;
     description: string;
@@ -1949,6 +1961,8 @@ export interface McpToolDefinition {
         properties: Record<string, unknown>;
         required?: string[];
     };
+    /** Set when the tool is deprecated and scheduled for removal in 4.0. */
+    deprecated?: ToolDeprecation;
 }
 export interface McpPromptArgument {
     name: string;

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "projscan",
   "mcpName": "io.github.abhiyoheswaran1/projscan",
-  "version": "3.7.0",
+  "version": "4.0.0",
   "description": "Agent-first code intelligence. MCP server (2025-03-26) with AST parsing for JavaScript, TypeScript, Python, Go, Java, Ruby, Rust, PHP, C#, Kotlin, Swift, and C++; repo understanding maps (projscan_understand), stable v3 semantic graph (projscan_semantic_graph), dataflow risk engine with bridge-helper detection (projscan_dataflow), code graph, file + per-function AST cyclomatic complexity, per-function fan-in + fan-out, coupling + cycle detection, structural PR diff with HTML reporter, coverage report with HTML reporter, intent-grounded one-call PR review (projscan_review with optional `intent` arg, new taint flows, contract changes, and newDataflowRisks) and long-running PR-watch mode with structured per-bucket deltas (projscan_review_watch), first-60-seconds workflow orientation (projscan_start), agent workplans (projscan_workplan), bug-hunt queues (projscan_bug_hunt), product-line planning (projscan_release_train), evidence packs (projscan_evidence_pack), regression planning (projscan_regression_plan), agent briefs (projscan_agent_brief), quality scorecards (projscan_quality_scorecard), and preflight with supply-chain IOC evidence, rule-driven fix suggestions + mechanical apply layer with rollback (projscan_apply_fix, projscan_fix_suggest, projscan_explain_issue), source-to-sink taint analysis (projscan_taint) with truncation reporting, transitive blast-radius analysis with cross-repo mode (projscan_impact for files and symbols), cross-repo workspace registration + intelligence (projscan_workspace_graph), per-function semantic search chunks (sub-file embeddings), per-rule confidence + severity drift + cost-summary analytics with live streaming (projscan_cost_summary), stable local analyzer + reporter plugin API (projscan_plugin, CLI --reporter, opt-in via PROJSCAN_PLUGINS_PREVIEW=1), monorepo workspace awareness with cross-package import policy + per-package dependencies / outdated / audit, BM25 + optional semantic search, cursor pagination, progress notifications, context-budgeted output, and a stable-surface CI guard. CLI on the side.",
   "type": "module",
   "main": "./dist/index.js",

package/dist/cli/commands/explain.d.ts

@@ -1 +0,0 @@
-export declare function registerExplain(): void;

package/dist/cli/commands/explain.js

@@ -1,42 +0,0 @@
-import chalk from 'chalk';
-import path from 'node:path';
-import { program, setupLogLevel, maybeCompactBanner, analyzeFile, assertFormatSupported } from '../_shared.js';
-import { reportExplanation } from '../../reporters/consoleReporter.js';
-import { reportExplanationJson } from '../../reporters/jsonReporter.js';
-import { reportExplanationMarkdown } from '../../reporters/markdownReporter.js';
-export function registerExplain() {
-    program
-        .command('explain <file>')
-        .description('Explain a file - its purpose, dependencies, and exports')
-        .action(async (filePath) => {
-        setupLogLevel();
-        maybeCompactBanner();
-        const format = assertFormatSupported('explain');
-        const absolutePath = path.resolve(filePath);
-        try {
-            const explanation = await analyzeFile(absolutePath);
-            switch (format) {
-                case 'json':
-                    reportExplanationJson(explanation);
-                    break;
-                case 'markdown':
-                    reportExplanationMarkdown(explanation);
-                    break;
-                default:
-                    reportExplanation(explanation);
-            }
-        }
-        catch (error) {
-            const message = error instanceof Error ? error.message : String(error);
-            if (error.code === 'ENOENT' || /not found/i.test(message)) {
-                console.error(chalk.red(`File not found: ${filePath}`));
-                console.error(chalk.dim(`  Tip: paths are repo-relative. Run \`projscan structure\` to see the file tree.`));
-            }
-            else {
-                console.error(chalk.red(message));
-            }
-            process.exit(1);
-        }
-    });
-}
-//# sourceMappingURL=explain.js.map

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

@@ -1 +0,0 @@
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package/dist/mcp/tools/explain.d.ts

@@ -1,2 +0,0 @@
-import { type McpTool } from './_shared.js';
-export declare const explainTool: McpTool;

package/dist/mcp/tools/explain.js

@@ -1,29 +0,0 @@
-import path from 'node:path';
-import { explainFile } from './_shared.js';
-export const explainTool = {
-    name: 'projscan_explain',
-    description: 'Explain a single file: purpose, imports, exports, and potential issues. Useful for understanding unfamiliar code before editing.',
-    inputSchema: {
-        type: 'object',
-        properties: {
-            file: {
-                type: 'string',
-                description: 'Path to the file relative to the project root.',
-            },
-        },
-        required: ['file'],
-    },
-    handler: async (args, rootPath) => {
-        const rel = typeof args.file === 'string' ? args.file : '';
-        if (!rel) {
-            throw new Error('file argument is required: pass a repo-relative path (e.g. "src/auth.ts").');
-        }
-        const absolutePath = path.resolve(rootPath, rel);
-        const resolvedRoot = path.resolve(rootPath);
-        if (!absolutePath.startsWith(resolvedRoot + path.sep) && absolutePath !== resolvedRoot) {
-            throw new Error(`file must be inside the project root (got "${rel}"; absolute or "../" paths are rejected for security).`);
-        }
-        return await explainFile(absolutePath, rootPath);
-    },
-};
-//# sourceMappingURL=explain.js.map

package/dist/mcp/tools/explain.js.map

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package/dist/mcp/tools/graph.d.ts

@@ -1,2 +0,0 @@
-import type { McpTool } from './_shared.js';
-export declare const graphTool: McpTool;

package/dist/mcp/tools/graph.js

@@ -1,74 +0,0 @@
-import { scanRepository } from '../../core/repositoryScanner.js';
-import { buildCodeGraph, filesImportingFile, filesImportingPackage, filesDefiningSymbol, exportsOf, importsOf, } from '../../core/codeGraph.js';
-import { loadCachedGraph, saveCachedGraph } from '../../core/indexCache.js';
-export const graphTool = {
-    name: 'projscan_graph',
-    description: 'Query the AST-based code graph directly. Returns imports, exports, importers, or symbol definitions for a file or symbol. Agents should prefer this over analyze/doctor/explain for targeted structural questions - it is much cheaper and more accurate.',
-    inputSchema: {
-        type: 'object',
-        properties: {
-            file: {
-                type: 'string',
-                description: 'File path (relative to project root) to query.',
-            },
-            symbol: {
-                type: 'string',
-                description: 'Symbol name to query (e.g. a function or class). Use instead of `file` to find where a symbol is defined.',
-            },
-            direction: {
-                type: 'string',
-                description: 'What to return: "imports" (what the file imports), "exports" (what the file exports), "importers" (who imports the file), "symbol_defs" (files defining the symbol), "package_importers" (files importing a package by name).',
-                enum: ['imports', 'exports', 'importers', 'symbol_defs', 'package_importers'],
-            },
-            limit: { type: 'number', description: 'Max entries returned (default 50).' },
-            max_tokens: { type: 'number', description: 'Cap the response to roughly this many tokens.' },
-        },
-        required: ['direction'],
-    },
-    handler: async (args, rootPath) => {
-        const scan = await scanRepository(rootPath);
-        const cached = await loadCachedGraph(rootPath);
-        const graph = await buildCodeGraph(rootPath, scan.files, cached);
-        await saveCachedGraph(rootPath, graph);
-        const direction = String(args.direction);
-        const file = typeof args.file === 'string' ? args.file : undefined;
-        const symbol = typeof args.symbol === 'string' ? args.symbol : undefined;
-        const limit = Math.max(1, Math.min(500, typeof args.limit === 'number' ? args.limit : 50));
-        switch (direction) {
-            case 'imports': {
-                if (!file) {
-                    throw new Error('direction=imports requires a `file` argument (repo-relative path, e.g. "src/auth.ts").');
-                }
-                return { file, imports: importsOf(graph, file).slice(0, limit) };
-            }
-            case 'exports': {
-                if (!file) {
-                    throw new Error('direction=exports requires a `file` argument (repo-relative path).');
-                }
-                return { file, exports: exportsOf(graph, file).slice(0, limit) };
-            }
-            case 'importers': {
-                if (!file) {
-                    throw new Error('direction=importers requires a `file` argument (repo-relative path).');
-                }
-                return { file, importers: filesImportingFile(graph, file).slice(0, limit) };
-            }
-            case 'symbol_defs': {
-                if (!symbol) {
-                    throw new Error('direction=symbol_defs requires a `symbol` argument (the exported name to look up, e.g. "authenticate").');
-                }
-                return { symbol, definedIn: filesDefiningSymbol(graph, symbol).slice(0, limit) };
-            }
-            case 'package_importers': {
-                const pkg = symbol ?? file;
-                if (!pkg) {
-                    throw new Error('direction=package_importers requires either `symbol` or `file` arg (the npm package name, e.g. "chalk").');
-                }
-                return { package: pkg, importers: filesImportingPackage(graph, pkg).slice(0, limit) };
-            }
-            default:
-                throw new Error(`unknown direction "${direction}". Valid: imports, exports, importers, symbol_defs, package_importers.`);
-        }
-    },
-};
-//# sourceMappingURL=graph.js.map

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