@lzehrung/codegraph 2.1.1 → 2.1.2

package/dist/cli/rootPolicy.js

@@ -1,11 +1,29 @@
 import fs from "node:fs";
+import path from "node:path";
 import { resolveFilePathFromRoot } from "../util/paths.js";
+// A slash- or backslash-prefixed path is drive-relative on Windows. Node resolves it
+// against the current drive, but resolveFilePathFromRoot leaves it unchanged because
+// path.posix considers it absolute. Route those non-UNC paths through path.win32.resolve
+// so later confinement checks receive a drive-qualified root.
+const WINDOWS_DRIVE_QUALIFIED_PATTERN = /^[A-Za-z]:[\\/]/;
+const WINDOWS_DRIVE_RELATIVE_ROOT_PATTERN = /^[\\/](?![\\/])/;
+function resolveAbsoluteProjectRoot(cwd, candidate) {
+    if (process.platform === "win32" &&
+        WINDOWS_DRIVE_RELATIVE_ROOT_PATTERN.test(candidate) &&
+        !WINDOWS_DRIVE_QUALIFIED_PATTERN.test(candidate)) {
+        return path.win32.resolve(cwd(), candidate);
+    }
+    return resolveFilePathFromRoot(cwd(), candidate);
+}
 export function looksLikeGlobPattern(baseRoot, value) {
     const hasGlobSyntax = /[*?]/.test(value) || (value.includes("{") && value.includes("}")) || (value.includes("[") && value.includes("]"));
     if (!hasGlobSyntax)
         return false;
     return !fs.existsSync(resolveFilePathFromRoot(baseRoot, value));
 }
+function invalidGlobRootMessage(command, value) {
+    return `Invalid ${command} path "${value}". Positional paths are scan roots, not glob patterns. Repeat --ignore-glob or --include-glob for each glob filter.`;
+}
 export function isExistingDirectory(filePath) {
     try {
         return fs.statSync(filePath, { throwIfNoEntry: false })?.isDirectory() ?? false;
@@ -53,7 +71,7 @@ export function assertValidIncludeRoots(command, baseRoot, includeRoots) {
     const globLikeRoot = includeRoots.find((includeRoot) => looksLikeGlobPattern(baseRoot, includeRoot));
     if (!globLikeRoot)
         return;
-    throw new Error(`Invalid ${command} path "${globLikeRoot}". Positional paths are scan roots, not glob patterns. Repeat --ignore-glob or --include-glob for each glob filter.`);
+    throw new Error(invalidGlobRootMessage(command, globLikeRoot));
 }
 export function parseNativeRuntimeMode(value) {
     if (value === undefined)
@@ -70,7 +88,7 @@ export function parseNativeRuntimeMode(value) {
  */
 export function resolveCliRootPolicy(input) {
     const { command, positionals, rootOpt, cwd } = input;
-    const resolveAbs = (p) => resolveFilePathFromRoot(cwd(), p);
+    const resolveAbs = (p) => resolveAbsoluteProjectRoot(cwd, p);
     if (command === "impact" && positionals.length) {
         const impactRootArg = positionals[0];
         const resolvedImpactRoot = resolveAbs(impactRootArg);
@@ -115,6 +133,21 @@ export function resolveCliRootPolicy(input) {
             messages: [`Invalid ${command} project root "${positionals[0]}". Expected an existing directory.`],
         };
     }
+    if (usesLegacyRootPositional(command) &&
+        !isLifecycleCommand(command) &&
+        !acceptsOptionalProjectRoot(command) &&
+        !rootOpt &&
+        firstPositionalRoot !== undefined &&
+        !isExistingDirectory(firstPositionalRoot)) {
+        const positional = positionals[0];
+        if (looksLikeGlobPattern(cwd(), positional)) {
+            return { status: "error", messages: [invalidGlobRootMessage(command, positional)] };
+        }
+        return {
+            status: "error",
+            messages: [`Invalid ${command} path "${positional}". Expected an existing directory or use --root <path>.`],
+        };
+    }
     const defaultProjectRoot = usesLegacyRootPositional(command) &&
         !rootOpt &&
         firstPositionalRoot !== undefined &&
@@ -183,7 +216,7 @@ export function resolveCliIncludeRoots(input) {
         return [...positionals];
     }
     if (positionals.length === 1 && looksLikeGlobPattern(cwd(), positionals[0])) {
-        throw new Error(`Invalid ${command} path "${positionals[0]}". Positional paths are scan roots, not glob patterns. Repeat --ignore-glob or --include-glob for each glob filter.`);
+        throw new Error(invalidGlobRootMessage(command, positionals[0]));
     }
     return [];
 }

package/dist/cli/rootPolicy.js.map

@@ -1 +1 @@
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package/dist/cli/skill.js

@@ -192,7 +192,7 @@ export async function handleSkillCommand(context) {
         if (!bundledSkillDir) {
             throw new Error("Bundled codegraph skill assets were not found.");
         }
-        context.writeStdoutLine(normalizePathForDisplay(bundledSkillDir));
+        writeCliOutput(context, normalizePathForDisplay(bundledSkillDir));
         return;
     }
     if (subcommand === "doctor") {

package/dist/cli/skill.js.map

@@ -1 +1 @@
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package/dist/cli/sql.js

@@ -26,7 +26,7 @@ export async function handleSqlCommand(context) {
     const queryText = context.getOpt("--query") ?? context.positionals[1];
     if (!dbOpt || !queryText) {
         context.writeStderrLine('Usage: sql <sqlite-path> "SELECT ..." OR sql --db <sqlite-path> --query "SELECT ..."');
-        context.exit(1);
+        context.exit(2);
     }
     const dbPath = path.isAbsolute(dbOpt)
         ? normalizePath(dbOpt)

package/dist/cli/symbols.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"symbols.d.ts","sourceRoot":"","sources":["../../src/cli/symbols.ts"],"names":[],"mappings":"AAEA,OAAO,EAAiB,KAAK,sBAAsB,EAAE,MAAM,cAAc,CAAC;AAI1E,MAAM,MAAM,qBAAqB,GAAG,sBAAsB,CAAC;AAyB3D,wBAAsB,oBAAoB,CAAC,OAAO,EAAE,qBAAqB,GAAG,OAAO,CAAC,IAAI,CAAC,CAkCxF"}
+{"version":3,"file":"symbols.d.ts","sourceRoot":"","sources":["../../src/cli/symbols.ts"],"names":[],"mappings":"AAEA,OAAO,EAAiB,KAAK,sBAAsB,EAAE,MAAM,cAAc,CAAC;AAI1E,MAAM,MAAM,qBAAqB,GAAG,sBAAsB,CAAC;AAyB3D,wBAAsB,oBAAoB,CAAC,OAAO,EAAE,qBAAqB,GAAG,OAAO,CAAC,IAAI,CAAC,CAoCxF"}

package/dist/cli/symbols.js

@@ -23,11 +23,13 @@ function parseWorkspaceSymbolKinds(rawValue) {
 export async function handleSymbolsCommand(context) {
     const query = context.positionals.join(" ").trim();
     let kinds;
+    let limit;
     try {
         kinds = parseWorkspaceSymbolKinds(context.getOpt("--kind"));
+        limit = parseBoundedIntegerOption(context.getOpt("--limit"), "--limit", 50, 0, 500);
     }
     catch (error) {
-        exitWithError(context, error, 1);
+        exitWithError(context, error, 2);
     }
     const fileGlob = context.getOpt("--file-glob");
     if (!query && !kinds?.length && !fileGlob) {
@@ -43,7 +45,7 @@ export async function handleSymbolsCommand(context) {
             ...(context.hasFlag("--exported") ? { exportedOnly: true } : {}),
             ...(context.hasFlag("--include-imports") ? { includeImports: true } : {}),
             ...(fileGlob !== undefined ? { fileGlob } : {}),
-            limit: parseBoundedIntegerOption(context.getOpt("--limit"), "--limit", 50, 0, 500),
+            limit,
         });
         if (context.hasFlag("--json")) {
             context.writeJSONLine(response);

package/dist/cli/symbols.js.map

@@ -1 +1 @@
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+{"version":3,"file":"symbols.js","sourceRoot":"","sources":["../../src/cli/symbols.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,8BAA8B,EAAE,gBAAgB,EAAE,MAAM,8BAA8B,CAAC;AAChG,OAAO,EAAE,UAAU,EAAE,MAAM,qBAAqB,CAAC;AACjD,OAAO,EAAE,aAAa,EAA+B,MAAM,cAAc,CAAC;AAC1E,OAAO,EAAE,iBAAiB,EAAE,MAAM,WAAW,CAAC;AAC9C,OAAO,EAAE,yBAAyB,EAAE,MAAM,cAAc,CAAC;AAIzD,MAAM,4BAA4B,GAAiB,MAAM,CAAC,MAAM,CAAC,UAAU,CAAC,CAAC;AAC7E,MAAM,+BAA+B,GAAwB,IAAI,GAAG,CAAC,4BAA4B,CAAC,CAAC;AAEnG,SAAS,qBAAqB,CAAC,KAAa;IAC1C,OAAO,+BAA+B,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC;AACpD,CAAC;AAED,SAAS,yBAAyB,CAAC,QAA4B;IAC7D,IAAI,QAAQ,KAAK,SAAS;QAAE,OAAO,SAAS,CAAC;IAC7C,MAAM,MAAM,GAAG,QAAQ;SACpB,KAAK,CAAC,GAAG,CAAC;SACV,GAAG,CAAC,CAAC,KAAK,EAAE,EAAE,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC;SAC5B,MAAM,CAAC,OAAO,CAAC,CAAC;IACnB,IAAI,CAAC,MAAM,CAAC,MAAM,IAAI,MAAM,CAAC,IAAI,CAAC,CAAC,KAAK,EAAE,EAAE,CAAC,CAAC,qBAAqB,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC;QAC5E,MAAM,IAAI,KAAK,CACb,yBAAyB,QAAQ,0CAA0C,4BAA4B,CAAC,IAAI,CAC1G,IAAI,CACL,GAAG,CACL,CAAC;IACJ,CAAC;IACD,OAAO,MAAM,CAAC,MAAM,CAAC,qBAAqB,CAAC,CAAC;AAC9C,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,oBAAoB,CAAC,OAA8B;IACvE,MAAM,KAAK,GAAG,OAAO,CAAC,WAAW,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC;IACnD,IAAI,KAA+B,CAAC;IACpC,IAAI,KAAa,CAAC;IAClB,IAAI,CAAC;QACH,KAAK,GAAG,yBAAyB,CAAC,OAAO,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAC,CAAC;QAC5D,KAAK,GAAG,yBAAyB,CAAC,OAAO,CAAC,MAAM,CAAC,SAAS,CAAC,EAAE,SAAS,EAAE,EAAE,EAAE,CAAC,EAAE,GAAG,CAAC,CAAC;IACtF,CAAC;IAAC,OAAO,KAAc,EAAE,CAAC;QACxB,aAAa,CAAC,OAAO,EAAE,KAAK,EAAE,CAAC,CAAC,CAAC;IACnC,CAAC;IACD,MAAM,QAAQ,GAAG,OAAO,CAAC,MAAM,CAAC,aAAa,CAAC,CAAC;IAC/C,IAAI,CAAC,KAAK,IAAI,CAAC,KAAK,EAAE,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAC;QAC1C,OAAO,CAAC,eAAe,CAAC,iBAAiB,CAAC,OAAO,EAAE,CAAC,CAAC;QACrD,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;IAClB,CAAC;IAED,IAAI,CAAC;QACH,MAAM,QAAQ,GAAG,MAAM,gBAAgB,CAAC;YACtC,IAAI,EAAE,OAAO,CAAC,IAAI;YAClB,KAAK;YACL,GAAG,CAAC,OAAO,CAAC,YAAY,CAAC,CAAC,CAAC,EAAE,YAAY,EAAE,OAAO,CAAC,YAAY,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;YACvE,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,KAAK,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;YAC3B,GAAG,CAAC,OAAO,CAAC,OAAO,CAAC,YAAY,CAAC,CAAC,CAAC,CAAC,EAAE,YAAY,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;YAChE,GAAG,CAAC,OAAO,CAAC,OAAO,CAAC,mBAAmB,CAAC,CAAC,CAAC,CAAC,EAAE,cAAc,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;YACzE,GAAG,CAAC,QAAQ,KAAK,SAAS,CAAC,CAAC,CAAC,EAAE,QAAQ,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;YAC/C,KAAK;SACN,CAAC,CAAC;QAEH,IAAI,OAAO,CAAC,OAAO,CAAC,QAAQ,CAAC,EAAE,CAAC;YAC9B,OAAO,CAAC,aAAa,CAAC,QAAQ,CAAC,CAAC;QAClC,CAAC;aAAM,CAAC;YACN,OAAO,CAAC,eAAe,CAAC,8BAA8B,CAAC,QAAQ,CAAC,CAAC,CAAC;QACpE,CAAC;IACH,CAAC;IAAC,OAAO,KAAc,EAAE,CAAC;QACxB,aAAa,CAAC,OAAO,EAAE,KAAK,EAAE,CAAC,CAAC,CAAC;IACnC,CAAC;AACH,CAAC"}

package/dist/cli.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"cli.d.ts","sourceRoot":"","sources":["../src/cli.ts"],"names":[],"mappings":";AAMA,OAAO,EASL,KAAK,UAAU,EAChB,MAAM,kBAAkB,CAAC;AAQ1B,OAAO,EAAE,oBAAoB,IAAI,gCAAgC,EAAE,MAAM,yBAAyB,CAAC;AACnG,eAAO,MAAM,yBAAyB,yhBAkD5B,CAAC;AA6GX,wBAAsB,MAAM,CAC1B,OAAO,GAAE,MAAM,EAA0B,EACzC,OAAO,GAAE,OAAO,CAAC,UAAU,CAAM,GAChC,OAAO,CAAC,IAAI,CAAC,CAEf;AAED,wBAAsB,IAAI,CAAC,OAAO,GAAE,MAAM,EAA0B,GAAG,OAAO,CAAC,IAAI,CAAC,CAWnF"}
+{"version":3,"file":"cli.d.ts","sourceRoot":"","sources":["../src/cli.ts"],"names":[],"mappings":";AAMA,OAAO,EASL,KAAK,UAAU,EAChB,MAAM,kBAAkB,CAAC;AAQ1B,OAAO,EAAE,oBAAoB,IAAI,gCAAgC,EAAE,MAAM,yBAAyB,CAAC;AACnG,eAAO,MAAM,yBAAyB,yhBAkD5B,CAAC;AA6HX,wBAAsB,MAAM,CAC1B,OAAO,GAAE,MAAM,EAA0B,EACzC,OAAO,GAAE,OAAO,CAAC,UAAU,CAAM,GAChC,OAAO,CAAC,IAAI,CAAC,CAEf;AAED,wBAAsB,IAAI,CAAC,OAAO,GAAE,MAAM,EAA0B,GAAG,OAAO,CAAC,IAAI,CAAC,CAWnF"}

package/dist/cli.js

@@ -90,7 +90,27 @@ async function runCliWithActiveRuntime(rawArgs) {
     }
     if (rawArgs[0] === "help") {
         const command = rawArgs[1];
-        writeStdoutLine((command ? helpTextForCommand(command, rawArgs.slice(2)) : CLI_HELP_TEXT)?.trimEnd() ?? CLI_HELP_TEXT);
+        if (!command) {
+            writeStdoutLine(CLI_HELP_TEXT.trimEnd());
+            return;
+        }
+        if (!isKnownCliCommand(command)) {
+            writeStderrLine(`Unknown command "${command}".`);
+            const suggestions = suggestCliCommands(command);
+            if (suggestions.length)
+                writeStderrLine(`Did you mean: ${suggestions.join(", ")}?`);
+            exitCli(2);
+        }
+        let helpParsed;
+        try {
+            helpParsed = parseCliArgs(command, rawArgs.slice(2));
+            validateCliArgs(command, helpParsed);
+        }
+        catch (error) {
+            writeStderrLine(errorMessage(error));
+            exitCli(2);
+        }
+        writeStdoutLine((helpTextForCommand(command, helpParsed.positionals) ?? CLI_HELP_TEXT).trimEnd());
         return;
     }
     const commandWasExplicit = Boolean(rawArgs[0] && !rawArgs[0].startsWith("-"));
@@ -105,20 +125,6 @@ async function runCliWithActiveRuntime(rawArgs) {
         exitCli(2);
     }
     const { getOpt, hasFlag } = createCliOptionAccessors(parsed);
-    if (hasFlag("--help") || hasFlag("-h")) {
-        const commandHelp = commandWasExplicit ? helpTextForCommand(cmd, parsed.positionals) : undefined;
-        writeStdoutLine((commandHelp ?? CLI_HELP_TEXT).trimEnd());
-        return;
-    }
-    if (hasFlag("--version") || hasFlag("-v")) {
-        if (hasFlag("--json")) {
-            writeJSONLine(getCodegraphPackageIdentity());
-        }
-        else {
-            writeStdoutLine(getCodegraphVersion());
-        }
-        return;
-    }
     if (!isKnownCliCommand(cmd)) {
         writeStderrLine(`Unknown command "${cmd}".`);
         const suggestions = suggestCliCommands(cmd);
@@ -127,7 +133,7 @@ async function runCliWithActiveRuntime(rawArgs) {
         const route = routeForCliIntent(cmd);
         if (route)
             writeStderrLine(`Try: ${route}`);
-        exitCli(1);
+        exitCli(2);
         return;
     }
     try {
@@ -137,6 +143,20 @@ async function runCliWithActiveRuntime(rawArgs) {
         writeStderrLine(errorMessage(error));
         exitCli(2);
     }
+    if (hasFlag("--help") || hasFlag("-h")) {
+        const commandHelp = commandWasExplicit ? helpTextForCommand(cmd, parsed.positionals) : undefined;
+        writeStdoutLine((commandHelp ?? CLI_HELP_TEXT).trimEnd());
+        return;
+    }
+    if (hasFlag("--version") || hasFlag("-v")) {
+        if (hasFlag("--json")) {
+            writeJSONLine(getCodegraphPackageIdentity());
+        }
+        else {
+            writeStdoutLine(getCodegraphVersion());
+        }
+        return;
+    }
     if (cmd === "viewer") {
         // Keep the human-only browser server out of normal agent command startup.
         const { handleViewerCommand } = await import("./cli/viewer.js");

package/dist/cli.js.map

@@ -1 +1 @@
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package/dist/documentLinks/check.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"check.d.ts","sourceRoot":"","sources":["../../src/documentLinks/check.ts"],"names":[],"mappings":"AAKA,OAAO,EAAoB,KAAK,2BAA2B,EAAE,MAAM,yBAAyB,CAAC;AAE7F,KAAK,yBAAyB,GAAG;IAC/B,IAAI,EAAE,MAAM,CAAC;IACb,MAAM,EAAE,MAAM,CAAC;CAChB,CAAC;AAEF,KAAK,sBAAsB,GAAG;IAC5B,KAAK,EAAE,yBAAyB,CAAC;IACjC,GAAG,EAAE,yBAAyB,CAAC;CAChC,CAAC;AAEF,MAAM,MAAM,8BAA8B,GAAG,cAAc,GAAG,mBAAmB,GAAG,kBAAkB,GAAG,cAAc,CAAC;AAExH,MAAM,MAAM,wBAAwB,GAAG;IACrC,IAAI,EAAE,MAAM,CAAC;IACb,KAAK,EAAE,sBAAsB,CAAC;IAC9B,GAAG,EAAE,MAAM,CAAC;IACZ,MAAM,EAAE,8BAA8B,CAAC;IACvC,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB,CAAC;AAEF,MAAM,MAAM,uBAAuB,GAAG;IACpC,aAAa,EAAE,CAAC,CAAC;IACjB,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE;QACP,YAAY,EAAE,MAAM,CAAC;QACrB,YAAY,EAAE,MAAM,CAAC;QACrB,eAAe,EAAE,MAAM,CAAC;QACxB,QAAQ,EAAE,MAAM,CAAC;KAClB,CAAC;IACF,QAAQ,EAAE,wBAAwB,EAAE,CAAC;CACtC,CAAC;AAYF,wBAAsB,kBAAkB,CACtC,WAAW,EAAE,MAAM,EACnB,SAAS,CAAC,EAAE,2BAA2B,GACtC,OAAO,CAAC,uBAAuB,CAAC,CAGlC;AAED,wBAAsB,yBAAyB,CAC7C,WAAW,EAAE,MAAM,EACnB,KAAK,EAAE,QAAQ,CAAC,MAAM,CAAC,GACtB,OAAO,CAAC,uBAAuB,CAAC,CAqElC"}
+{"version":3,"file":"check.d.ts","sourceRoot":"","sources":["../../src/documentLinks/check.ts"],"names":[],"mappings":"AAKA,OAAO,EAAoB,KAAK,2BAA2B,EAAE,MAAM,yBAAyB,CAAC;AAE7F,KAAK,yBAAyB,GAAG;IAC/B,IAAI,EAAE,MAAM,CAAC;IACb,MAAM,EAAE,MAAM,CAAC;CAChB,CAAC;AAEF,KAAK,sBAAsB,GAAG;IAC5B,KAAK,EAAE,yBAAyB,CAAC;IACjC,GAAG,EAAE,yBAAyB,CAAC;CAChC,CAAC;AAEF,MAAM,MAAM,8BAA8B,GAAG,cAAc,GAAG,mBAAmB,GAAG,kBAAkB,GAAG,cAAc,CAAC;AAExH,MAAM,MAAM,wBAAwB,GAAG;IACrC,IAAI,EAAE,MAAM,CAAC;IACb,KAAK,EAAE,sBAAsB,CAAC;IAC9B,GAAG,EAAE,MAAM,CAAC;IACZ,MAAM,EAAE,8BAA8B,CAAC;IACvC,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB,CAAC;AAEF,MAAM,MAAM,uBAAuB,GAAG;IACpC,aAAa,EAAE,CAAC,CAAC;IACjB,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE;QACP,YAAY,EAAE,MAAM,CAAC;QACrB,YAAY,EAAE,MAAM,CAAC;QACrB,eAAe,EAAE,MAAM,CAAC;QACxB,QAAQ,EAAE,MAAM,CAAC;KAClB,CAAC;IACF,QAAQ,EAAE,wBAAwB,EAAE,CAAC;CACtC,CAAC;AAYF,wBAAsB,kBAAkB,CACtC,WAAW,EAAE,MAAM,EACnB,SAAS,CAAC,EAAE,2BAA2B,GACtC,OAAO,CAAC,uBAAuB,CAAC,CAGlC;AAED,wBAAsB,yBAAyB,CAC7C,WAAW,EAAE,MAAM,EACnB,KAAK,EAAE,QAAQ,CAAC,MAAM,CAAC,GACtB,OAAO,CAAC,uBAAuB,CAAC,CAgFlC"}

package/dist/documentLinks/check.js

@@ -13,8 +13,19 @@ export async function checkMarkdownLinks(projectRoot, discovery) {
 export async function checkMarkdownLinksInFiles(projectRoot, files) {
     const root = path.resolve(projectRoot);
     const realRoot = await fsp.realpath(root);
-    const markdownFiles = Array.from(new Set(Array.from(files, (file) => path.resolve(root, file))))
-        .filter((file) => isFilePathWithinRoot(root, file))
+    const markdownFileCandidates = await Promise.all(Array.from(files, async (file) => {
+        const absoluteFile = path.resolve(root, file);
+        if (isFilePathWithinRoot(root, absoluteFile))
+            return path.resolve(realRoot, path.relative(root, absoluteFile));
+        try {
+            return await fsp.realpath(absoluteFile);
+        }
+        catch {
+            return absoluteFile;
+        }
+    }));
+    const markdownFiles = Array.from(new Set(markdownFileCandidates))
+        .filter((file) => isFilePathWithinRoot(realRoot, file))
         .filter((file) => supportForFile(file)?.id === "markdown");
     const targetStatusByPath = new Map();
     const anchorsByPath = new Map();
@@ -28,7 +39,7 @@ export async function checkMarkdownLinksInFiles(projectRoot, files) {
         for (const occurrence of occurrences) {
             if ("missingReference" in occurrence) {
                 linksChecked += 1;
-                failures.push(toFailure(root, displayFile, occurrence, "missing_reference"));
+                failures.push(toFailure(realRoot, displayFile, occurrence, "missing_reference"));
                 continue;
             }
             const target = parseLocalLinkTarget(occurrence.destination);
@@ -40,25 +51,25 @@ export async function checkMarkdownLinksInFiles(projectRoot, files) {
                 continue;
             }
             linksChecked += 1;
-            const resolvedTarget = resolveMarkdownTarget(root, file, target.path);
-            if (!isFilePathWithinRoot(root, resolvedTarget)) {
-                failures.push(toFailure(root, displayFile, occurrence, "outside_root", resolvedTarget));
+            const resolvedTarget = resolveMarkdownTarget(realRoot, file, target.path);
+            if (!isFilePathWithinRoot(realRoot, resolvedTarget)) {
+                failures.push(toFailure(realRoot, displayFile, occurrence, "outside_root", resolvedTarget));
                 continue;
             }
             const targetStatus = await cachedTargetStatus(resolvedTarget, targetStatusByPath);
             if (targetStatus.status === "missing") {
-                failures.push(toFailure(root, displayFile, occurrence, "missing_file", resolvedTarget));
+                failures.push(toFailure(realRoot, displayFile, occurrence, "missing_file", resolvedTarget));
                 continue;
             }
             if (!isFilePathWithinRoot(realRoot, targetStatus.realPath)) {
-                failures.push(toFailure(root, displayFile, occurrence, "outside_root", resolvedTarget));
+                failures.push(toFailure(realRoot, displayFile, occurrence, "outside_root", resolvedTarget));
                 continue;
             }
             if (!target.fragment || targetStatus.isDirectory || supportForFile(resolvedTarget)?.id !== "markdown")
                 continue;
             const anchors = await cachedMarkdownAnchors(targetStatus.realPath, anchorsByPath);
             if (!anchors.has(target.fragment)) {
-                failures.push(toFailure(root, displayFile, occurrence, "missing_fragment", resolvedTarget));
+                failures.push(toFailure(realRoot, displayFile, occurrence, "missing_fragment", resolvedTarget));
             }
         }
     }

package/dist/documentLinks/check.js.map

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package/dist/duplicates/types.d.ts

@@ -82,6 +82,8 @@ export type DuplicateDetectionOptions = {
     maxTokens?: number;
     maxBucketSize?: number;
     maxPairs?: number;
+    /** Count candidate duplicate groups without scoring every pair. */
+    countOnly?: boolean;
     shingleSize?: number;
     windowSize?: number;
     includeRawPairs?: boolean;

package/dist/duplicates/types.d.ts.map

@@ -1 +1 @@
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package/dist/duplicates/units.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"units.d.ts","sourceRoot":"","sources":["../../src/duplicates/units.ts"],"names":[],"mappings":"AAIA,OAAO,EAAmC,KAAK,KAAK,EAAE,MAAM,0BAA0B,CAAC;AAQvF,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,6BAA6B,CAAC;AAErE,OAAO,EAAc,KAAK,YAAY,EAAE,KAAK,SAAS,EAAE,MAAM,qBAAqB,CAAC;AAQpF,OAAO,KAAK,EAAE,cAAc,EAAkB,MAAM,uBAAuB,CAAC;AAY5E,OAAO,KAAK,EACV,uBAAuB,EACvB,mBAAmB,EACnB,wBAAwB,EACxB,qBAAqB,EACrB,8BAA8B,EAC9B,kBAAkB,EAClB,gBAAgB,EAEjB,MAAM,YAAY,CAAC;AAEpB,eAAO,MAAM,wBAAwB,MAAM,CAAC;AAC5C,wBAAgB,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,gBAAgB,EAAE,WAAW,GAAG,SAAS,CAAC,GAAG,MAAM,CAEtF;AA8BD,wBAAgB,aAAa,CAAC,KAAK,EAAE,MAAM,GAAG,MAAM,CAEnD;AAkDD,wBAAgB,wBAAwB,CAAC,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,GAAG,MAAM,CAEzF;AAUD,wBAAgB,2BAA2B,CAAC,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,GAAG,MAAM,CAE5G;AAED,wBAAgB,sBAAsB,CAAC,QAAQ,EAAE,MAAM,EAAE,WAAW,EAAE,MAAM,GAAG,SAAS,GAAG,MAAM,CAGhG;AAMD,wBAAgB,yBAAyB,CAAC,IAAI,EAAE,MAAM,EAAE,UAAU,EAAE,YAAY,CAAC,YAAY,CAAC,GAAG,SAAS,GAAG,MAAM,EAAE,CAKpH;AAED,wBAAgB,kBAAkB,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,EAAE,CAKzD;AAED,wBAAgB,yBAAyB,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,EAAE,CAMhE;AAED,wBAAgB,wBAAwB,CAAC,SAAS,EAAE,MAAM,GAAG,OAAO,CAQnE;AAED,wBAAgB,wBAAwB,CAAC,SAAS,EAAE,MAAM,GAAG,OAAO,CAKnE;AAED,wBAAgB,uBAAuB,CAAC,IAAI,EAAE,MAAM,GAAG;IAAE,mBAAmB,EAAE,OAAO,CAAC;IAAC,eAAe,EAAE,OAAO,CAAA;CAAE,CAQhH;AAED,6EAA6E;AAC7E,wBAAgB,iBAAiB,CAC/B,IAAI,EAAE,kBAAkB,EACxB,YAAY,EAAE,MAAM,EACpB,IAAI,EAAE,MAAM,EACZ,WAAW,EAAE,MAAM,EACnB,UAAU,EAAE,MAAM,EAClB,UAAU,EAAE,YAAY,CAAC,YAAY,CAAC,GAAG,SAAS,EAClD,OAAO,GAAE;IAAE,YAAY,CAAC,EAAE,MAAM,CAAC;IAAC,SAAS,CAAC,EAAE,MAAM,CAAA;CAAO,EAC3D,YAAY,CAAC,EAAE,MAAM,GACpB,qBAAqB,CA0BvB;AAED,wBAAgB,cAAc,CAC5B,MAAM,EAAE,SAAS,EACjB,KAAK,EAAE,KAAK,EACZ,WAAW,EAAE,MAAM,GAAG,SAAS,EAC/B,UAAU,EAAE,YAAY,CAAC,YAAY,CAAC,GAAG,SAAS,EAClD,WAAW,EAAE,MAAM,EACnB,UAAU,EAAE,MAAM,EAClB,UAAU,EAAE,mBAAmB,GAAG,SAAS,GAC1C,qBAAqB,GAAG,SAAS,CA+BnC;AAED,wBAAgB,mBAAmB,CACjC,QAAQ,EAAE,MAAM,EAChB,UAAU,EAAE,MAAM,EAClB,QAAQ,EAAE,OAAO,EACjB,MAAM,EAAE,MAAM,EACd,SAAS,EAAE,MAAM,EACjB,SAAS,EAAE,MAAM,GAChB,KAAK,EAAE,CAMT;AAED,wBAAgB,8BAA8B,CAC5C,QAAQ,EAAE,MAAM,EAChB,UAAU,EAAE,MAAM,EAClB,QAAQ,EAAE,OAAO,EACjB,MAAM,EAAE,MAAM,EACd,SAAS,EAAE,MAAM,EACjB,SAAS,EAAE,MAAM,GAChB;IAAE,MAAM,EAAE,KAAK,EAAE,CAAC;IAAC,YAAY,EAAE,KAAK,EAAE,CAAA;CAAE,CAc5C;AAED,wBAAgB,sBAAsB,CACpC,QAAQ,EAAE,MAAM,EAChB,UAAU,EAAE,MAAM,EAClB,QAAQ,EAAE,OAAO,EACjB,MAAM,EAAE,MAAM,EACd,SAAS,EAAE,MAAM,GAChB,KAAK,EAAE,CAGT;AAED,wBAAgB,kBAAkB,CAAC,MAAM,EAAE,SAAS,EAAE,MAAM,EAAE,SAAS,KAAK,EAAE,GAAG,KAAK,GAAG,SAAS,CAWjG;AAED,wBAAsB,sBAAsB,CAC1C,KAAK,EAAE,YAAY,EACnB,IAAI,EAAE,MAAM,EACZ,MAAM,EAAE,MAAM,EACd,KAAK,EAAE,wBAAwB,GAC9B,OAAO,CAAC,mBAAmB,GAAG,SAAS,CAAC,CA+B1C;AAED,wBAAgB,oBAAoB,CAAC,MAAM,EAAE,iBAAiB,GAAG,mBAAmB,CAMnF;AAED,wBAAgB,oBAAoB,CAClC,OAAO,EAAE,mBAAmB,GAAG,SAAS,EACxC,SAAS,EAAE,MAAM,EACjB,OAAO,EAAE,MAAM,GACd,MAAM,GAAG,SAAS,CASpB;AAED,wBAAgB,oBAAoB,CAClC,OAAO,EAAE,mBAAmB,EAC5B,SAAS,EAAE,MAAM,EACjB,OAAO,EAAE,MAAM,GACd;IAAE,KAAK,EAAE,MAAM,CAAC;IAAC,GAAG,EAAE,MAAM,CAAA;CAAE,GAAG,SAAS,CAgB5C;AAED,wBAAgB,wBAAwB,CACtC,IAAI,EAAE,cAAc,EACpB,UAAU,EAAE,MAAM,EAClB,QAAQ,EAAE,MAAM,GACf,cAAc,GAAG,IAAI,CAQvB;AAED,wBAAgB,kBAAkB,CAAC,IAAI,EAAE,cAAc,GAAG,MAAM,CAe/D;AAED,wBAAgB,qBAAqB,CAAC,IAAI,EAAE,cAAc,GAAG,OAAO,CAGnE;AAED,wBAAgB,oBAAoB,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CASzD;AAED,4EAA4E;AAC5E,wBAAgB,cAAc,CAC5B,QAAQ,EAAE,MAAM,EAChB,MAAM,EAAE,SAAS,KAAK,EAAE,EACxB,WAAW,EAAE,MAAM,GAAG,SAAS,EAC/B,UAAU,EAAE,YAAY,CAAC,YAAY,CAAC,GAAG,SAAS,EAClD,WAAW,EAAE,MAAM,EACnB,UAAU,EAAE,MAAM,EAClB,UAAU,EAAE,mBAAmB,GAAG,SAAS,GAC1C,qBAAqB,EAAE,CAsBzB;AAED,wBAAgB,cAAc,CAAC,IAAI,EAAE,qBAAqB,EAAE,YAAY,EAAE,OAAO,EAAE,SAAS,EAAE,MAAM,GAAG,OAAO,CAG7G;AAED,iEAAiE;AACjE,wBAAsB,qBAAqB,CACzC,KAAK,EAAE,YAAY,EACnB,OAAO,EAAE,8BAA8B,GACtC,OAAO,CAAC,uBAAuB,CAAC,CA4DlC;AAED,wBAAsB,0BAA0B,CAC9C,KAAK,EAAE,YAAY,EACnB,IAAI,EAAE,MAAM,EACZ,WAAW,EAAE,MAAM,GAAG,SAAS,EAC/B,SAAS,EAAE,MAAM,EACjB,SAAS,EAAE,MAAM,EACjB,WAAW,EAAE,MAAM,EACnB,UAAU,EAAE,MAAM,EAClB,eAAe,EAAE,wBAAwB,GACxC,OAAO,CAAC,qBAAqB,EAAE,CAAC,CAgClC"}
+{"version":3,"file":"units.d.ts","sourceRoot":"","sources":["../../src/duplicates/units.ts"],"names":[],"mappings":"AAIA,OAAO,EAAmC,KAAK,KAAK,EAAE,MAAM,0BAA0B,CAAC;AAQvF,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,6BAA6B,CAAC;AAErE,OAAO,EAAc,KAAK,YAAY,EAAE,KAAK,SAAS,EAAE,MAAM,qBAAqB,CAAC;AAQpF,OAAO,KAAK,EAAE,cAAc,EAAkB,MAAM,uBAAuB,CAAC;AAkB5E,OAAO,KAAK,EACV,uBAAuB,EACvB,mBAAmB,EACnB,wBAAwB,EACxB,qBAAqB,EACrB,8BAA8B,EAC9B,kBAAkB,EAClB,gBAAgB,EAEjB,MAAM,YAAY,CAAC;AAEpB,eAAO,MAAM,wBAAwB,MAAM,CAAC;AAC5C,wBAAgB,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,gBAAgB,EAAE,WAAW,GAAG,SAAS,CAAC,GAAG,MAAM,CAEtF;AA8BD,wBAAgB,aAAa,CAAC,KAAK,EAAE,MAAM,GAAG,MAAM,CAEnD;AAkDD,wBAAgB,wBAAwB,CAAC,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,GAAG,MAAM,CAEzF;AAUD,wBAAgB,2BAA2B,CAAC,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,GAAG,MAAM,CAE5G;AAED,wBAAgB,sBAAsB,CAAC,QAAQ,EAAE,MAAM,EAAE,WAAW,EAAE,MAAM,GAAG,SAAS,GAAG,MAAM,CAMhG;AAMD,wBAAgB,yBAAyB,CAAC,IAAI,EAAE,MAAM,EAAE,UAAU,EAAE,YAAY,CAAC,YAAY,CAAC,GAAG,SAAS,GAAG,MAAM,EAAE,CAKpH;AAED,wBAAgB,kBAAkB,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,EAAE,CAKzD;AAED,wBAAgB,yBAAyB,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,EAAE,CAMhE;AAED,wBAAgB,wBAAwB,CAAC,SAAS,EAAE,MAAM,GAAG,OAAO,CAQnE;AAED,wBAAgB,wBAAwB,CAAC,SAAS,EAAE,MAAM,GAAG,OAAO,CAKnE;AAED,wBAAgB,uBAAuB,CAAC,IAAI,EAAE,MAAM,GAAG;IAAE,mBAAmB,EAAE,OAAO,CAAC;IAAC,eAAe,EAAE,OAAO,CAAA;CAAE,CAQhH;AAED,6EAA6E;AAC7E,wBAAgB,iBAAiB,CAC/B,IAAI,EAAE,kBAAkB,EACxB,YAAY,EAAE,MAAM,EACpB,IAAI,EAAE,MAAM,EACZ,WAAW,EAAE,MAAM,EACnB,UAAU,EAAE,MAAM,EAClB,UAAU,EAAE,YAAY,CAAC,YAAY,CAAC,GAAG,SAAS,EAClD,OAAO,GAAE;IAAE,YAAY,CAAC,EAAE,MAAM,CAAC;IAAC,SAAS,CAAC,EAAE,MAAM,CAAA;CAAO,EAC3D,YAAY,CAAC,EAAE,MAAM,GACpB,qBAAqB,CA0BvB;AAED,wBAAgB,cAAc,CAC5B,MAAM,EAAE,SAAS,EACjB,KAAK,EAAE,KAAK,EACZ,WAAW,EAAE,MAAM,GAAG,SAAS,EAC/B,UAAU,EAAE,YAAY,CAAC,YAAY,CAAC,GAAG,SAAS,EAClD,WAAW,EAAE,MAAM,EACnB,UAAU,EAAE,MAAM,EAClB,UAAU,EAAE,mBAAmB,GAAG,SAAS,GAC1C,qBAAqB,GAAG,SAAS,CA+BnC;AAED,wBAAgB,mBAAmB,CACjC,QAAQ,EAAE,MAAM,EAChB,UAAU,EAAE,MAAM,EAClB,QAAQ,EAAE,OAAO,EACjB,MAAM,EAAE,MAAM,EACd,SAAS,EAAE,MAAM,EACjB,SAAS,EAAE,MAAM,GAChB,KAAK,EAAE,CAMT;AAED,wBAAgB,8BAA8B,CAC5C,QAAQ,EAAE,MAAM,EAChB,UAAU,EAAE,MAAM,EAClB,QAAQ,EAAE,OAAO,EACjB,MAAM,EAAE,MAAM,EACd,SAAS,EAAE,MAAM,EACjB,SAAS,EAAE,MAAM,GAChB;IAAE,MAAM,EAAE,KAAK,EAAE,CAAC;IAAC,YAAY,EAAE,KAAK,EAAE,CAAA;CAAE,CAc5C;AAED,wBAAgB,sBAAsB,CACpC,QAAQ,EAAE,MAAM,EAChB,UAAU,EAAE,MAAM,EAClB,QAAQ,EAAE,OAAO,EACjB,MAAM,EAAE,MAAM,EACd,SAAS,EAAE,MAAM,GAChB,KAAK,EAAE,CAGT;AAED,wBAAgB,kBAAkB,CAAC,MAAM,EAAE,SAAS,EAAE,MAAM,EAAE,SAAS,KAAK,EAAE,GAAG,KAAK,GAAG,SAAS,CAWjG;AAED,wBAAsB,sBAAsB,CAC1C,KAAK,EAAE,YAAY,EACnB,IAAI,EAAE,MAAM,EACZ,MAAM,EAAE,MAAM,EACd,KAAK,EAAE,wBAAwB,GAC9B,OAAO,CAAC,mBAAmB,GAAG,SAAS,CAAC,CA+B1C;AAED,wBAAgB,oBAAoB,CAAC,MAAM,EAAE,iBAAiB,GAAG,mBAAmB,CAMnF;AAED,wBAAgB,oBAAoB,CAClC,OAAO,EAAE,mBAAmB,GAAG,SAAS,EACxC,SAAS,EAAE,MAAM,EACjB,OAAO,EAAE,MAAM,GACd,MAAM,GAAG,SAAS,CASpB;AAED,wBAAgB,oBAAoB,CAClC,OAAO,EAAE,mBAAmB,EAC5B,SAAS,EAAE,MAAM,EACjB,OAAO,EAAE,MAAM,GACd;IAAE,KAAK,EAAE,MAAM,CAAC;IAAC,GAAG,EAAE,MAAM,CAAA;CAAE,GAAG,SAAS,CAgB5C;AAED,wBAAgB,wBAAwB,CACtC,IAAI,EAAE,cAAc,EACpB,UAAU,EAAE,MAAM,EAClB,QAAQ,EAAE,MAAM,GACf,cAAc,GAAG,IAAI,CAQvB;AAED,wBAAgB,kBAAkB,CAAC,IAAI,EAAE,cAAc,GAAG,MAAM,CAe/D;AAED,wBAAgB,qBAAqB,CAAC,IAAI,EAAE,cAAc,GAAG,OAAO,CAGnE;AAED,wBAAgB,oBAAoB,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CASzD;AAED,4EAA4E;AAC5E,wBAAgB,cAAc,CAC5B,QAAQ,EAAE,MAAM,EAChB,MAAM,EAAE,SAAS,KAAK,EAAE,EACxB,WAAW,EAAE,MAAM,GAAG,SAAS,EAC/B,UAAU,EAAE,YAAY,CAAC,YAAY,CAAC,GAAG,SAAS,EAClD,WAAW,EAAE,MAAM,EACnB,UAAU,EAAE,MAAM,EAClB,UAAU,EAAE,mBAAmB,GAAG,SAAS,GAC1C,qBAAqB,EAAE,CAsBzB;AAED,wBAAgB,cAAc,CAAC,IAAI,EAAE,qBAAqB,EAAE,YAAY,EAAE,OAAO,EAAE,SAAS,EAAE,MAAM,GAAG,OAAO,CAG7G;AAED,iEAAiE;AACjE,wBAAsB,qBAAqB,CACzC,KAAK,EAAE,YAAY,EACnB,OAAO,EAAE,8BAA8B,GACtC,OAAO,CAAC,uBAAuB,CAAC,CA4DlC;AAED,wBAAsB,0BAA0B,CAC9C,KAAK,EAAE,YAAY,EACnB,IAAI,EAAE,MAAM,EACZ,WAAW,EAAE,MAAM,GAAG,SAAS,EAC/B,SAAS,EAAE,MAAM,EACjB,SAAS,EAAE,MAAM,EACjB,WAAW,EAAE,MAAM,EACnB,UAAU,EAAE,MAAM,EAClB,eAAe,EAAE,wBAAwB,GACxC,OAAO,CAAC,qBAAqB,EAAE,CAAC,CAgClC"}

package/dist/duplicates/units.js

@@ -12,7 +12,7 @@ import { prepareSourceInput } from "../languages/filePrep.js";
 import { getNativeDuplicateTokens, getNativeTreeSitterSupportedLanguageIds, isNativeDuplicateTokenizationAvailable, isNativeTreeSitterDisabledByEnv, } from "../native/treeSitterNative.js";
 import { maskJsLikeCommentsStringsAndRegex } from "../util/comments.js";
 import { collectLineStartOffsets } from "../util/lines.js";
-import { assertFilePathWithinRoot, fileIdentityKey, normalizePath, toProjectDisplayPath } from "../util/paths.js";
+import { assertFilePathWithinRoot, fileIdentityKey, normalizePath, toProjectDisplayPath, toProjectRelativePath, } from "../util/paths.js";
 import { logWithLevel } from "../logging.js";
 import { duplicateUnitCacheVariant, tryLoadDuplicateUnitsFromCache, writeDuplicateUnitsBatchToCache, writeDuplicateUnitsToCache, } from "./unitCache.js";
 export const DEFAULT_MAX_FINGERPRINTS = 128;
@@ -111,7 +111,11 @@ export function formatDuplicateSymbolHandle(file, name, line, column) {
 export function normalizeDetectionFile(filePath, projectRoot) {
     if (!projectRoot)
         return normalizePath(filePath);
-    return assertFilePathWithinRoot(projectRoot, filePath, "Duplicate input file");
+    const file = assertFilePathWithinRoot(projectRoot, filePath, "Duplicate input file");
+    const relativeFile = toProjectRelativePath(projectRoot, file);
+    if (relativeFile === null)
+        return file;
+    return normalizePath(path.resolve(projectRoot, relativeFile));
 }
 function internalUnitId(unit, absoluteFile) {
     return `${normalizePath(absoluteFile)}:${unit.startLine}:${unit.endLine}:${unit.kind}:${unit.name ?? ""}`;