dotmd-cli 0.40.0 → 0.40.2

package/bin/dotmd.mjs

@@ -335,15 +335,19 @@ Use --dry-run (-n) to preview changes without writing anything.`,
 
   check: `dotmd check — validate frontmatter and references
 
+By default the warning list is suppressed: you see counts plus a one-line
+pointer to \`dotmd doctor\` (auto-fix) or \`dotmd check --verbose\`
+(per-doc detail). Errors are always shown in full.
+
 Options:
-  --errors-only          Show only errors, suppress warnings
+  --verbose              Show every warning per-doc (with category collapse
+                         applied — high-frequency auto-fixable categories
+                         summarize to a one-line bulk-fix hint).
+  --no-collapse          Like --verbose but disables category collapse too —
+                         every warning prints raw.
+  --errors-only          Show only errors, suppress warnings entirely
   --fix                  Auto-fix broken refs, lint issues, and regenerate index
-  --json                 Output errors and warnings as JSON
-  --no-collapse          Show every warning per-doc (since 0.37.0, high-frequency
-                         auto-fixable warning categories — singular module/surface
-                         deprecations, updated-behind-git — are collapsed into a
-                         one-line summary with the bulk-fix command). --json output
-                         is unchanged regardless.
+  --json                 Output errors and warnings as JSON (always full detail)
   --dry-run, -n          Preview fixes without writing (with --fix)`,
 
   archive: `dotmd archive <file> — archive a document
@@ -1219,6 +1223,7 @@ async function main() {
     const fix = args.includes('--fix');
     const errorsOnly = args.includes('--errors-only');
     const noCollapse = args.includes('--no-collapse');
+    const verbose = args.includes('--verbose');
 
     if (fix) {
       // Auto-fix: broken refs, then lint, then rebuild index
@@ -1249,7 +1254,7 @@ async function main() {
           passed: freshIndex.errors.length === 0,
         }, null, 2) + '\n');
       } else {
-        process.stdout.write('\n' + renderCheck(freshIndex, config, { errorsOnly, noCollapse }));
+        process.stdout.write('\n' + renderCheck(freshIndex, config, { errorsOnly, noCollapse, verbose }));
       }
       if (freshIndex.errors.length > 0) process.exitCode = 1;
       return;
@@ -1268,7 +1273,7 @@ async function main() {
       return;
     }
 
-    process.stdout.write(renderCheck(index, config, { errorsOnly, noCollapse }));
+    process.stdout.write(renderCheck(index, config, { errorsOnly, noCollapse, verbose }));
     if (index.errors.length > 0) process.exitCode = 1;
     return;
   }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "dotmd-cli",
-  "version": "0.40.0",
+  "version": "0.40.2",
   "description": "CLI for managing markdown documents with YAML frontmatter — index, query, validate, graph, export, Notion sync, AI summaries.",
   "type": "module",
   "license": "MIT",

package/src/lifecycle.mjs

@@ -1,6 +1,6 @@
 import { existsSync, mkdirSync, readFileSync, writeFileSync } from 'node:fs';
 import path from 'node:path';
-import { extractFrontmatter, parseSimpleFrontmatter, replaceFrontmatter } from './frontmatter.mjs';
+import { extractFrontmatter, parseSimpleFrontmatter } from './frontmatter.mjs';
 import { asString, toRepoPath, die, warn, resolveDocPath, resolveRefPath, escapeRegex, nowIso, suggestCandidates, emitFilesFooter } from './util.mjs';
 import { gitMv, getGitLastModified, getGitLastModifiedBatch } from './git.mjs';
 import { buildIndex, collectDocFiles } from './index.mjs';
@@ -829,30 +829,40 @@ function updateRefsAfterMove(oldPath, newPath, config) {
 
   for (const docFile of allFiles) {
     if (docFile === newPath) continue;
-    let raw = readFileSync(docFile, 'utf8');
-    const { frontmatter: fm } = extractFrontmatter(raw);
-    if (!fm || !fm.includes(basename)) continue;
+    const raw = readFileSync(docFile, 'utf8');
+    if (!raw.includes(basename)) continue;
+    const { frontmatter: fm, body } = extractFrontmatter(raw);
+    if (!fm) continue;
 
     const docDir = path.dirname(docFile);
     const oldRelPath = path.relative(docDir, oldPath).split(path.sep).join('/');
     const newRelPath = path.relative(docDir, newPath).split(path.sep).join('/');
 
     let newFm = fm;
-
-    // Replace exact relative path
     if (newFm.includes(oldRelPath)) {
       newFm = newFm.split(oldRelPath).join(newRelPath);
     }
-
-    // Also handle ./ prefix variant
     const dotSlashOld = './' + oldRelPath;
     if (newFm.includes(dotSlashOld)) {
       newFm = newFm.split(dotSlashOld).join(newRelPath);
     }
 
-    if (newFm !== fm) {
-      raw = replaceFrontmatter(raw, newFm);
-      writeFileSync(docFile, raw, 'utf8');
+    // Body markdown links [text](path.md) or [text](path.md#anchor) pointing
+    // at oldPath. resolveRefPath can't be used here: oldPath no longer exists
+    // on disk (git mv already ran), so its existsSync probe would fail. Match
+    // by resolving the href manually and comparing absolute paths instead.
+    const linkRegex = /(\[[^\]]*\]\()([^)#]+\.md)(#[^)]*)?(\))/g;
+    const newBody = body.replace(linkRegex, (match, pre, href, frag, post) => {
+      if (/^https?:/i.test(href)) return match;
+      const docRelAbs = path.resolve(docDir, href);
+      const repoRelAbs = path.resolve(config.repoRoot, href);
+      if (docRelAbs !== oldPath && repoRelAbs !== oldPath) return match;
+      const newHref = path.relative(docDir, newPath).split(path.sep).join('/');
+      return `${pre}${newHref}${frag ?? ''}${post}`;
+    });
+
+    if (newFm !== fm || newBody !== body) {
+      writeFileSync(docFile, `---\n${newFm}\n---\n${newBody}`, 'utf8');
       touched.push(docFile);
     }
   }
@@ -895,10 +905,7 @@ function updateRefsFromMovedFile(oldPath, newPath, config) {
   });
 
   if (newFm !== frontmatter || newBody !== body) {
-    const rebuilt = replaceFrontmatter(raw, newFm);
-    // Replace body: rebuilt has updated frontmatter but old body
-    const { frontmatter: updatedFm } = extractFrontmatter(rebuilt);
-    writeFileSync(newPath, `---\n${updatedFm}\n---${newBody}`, 'utf8');
+    writeFileSync(newPath, `---\n${newFm}\n---\n${newBody}`, 'utf8');
     return 1;
   }
 
@@ -913,14 +920,27 @@ function countRefsToUpdate(oldPath, newPath, config) {
   for (const docFile of allFiles) {
     if (docFile === newPath) continue;
     const raw = readFileSync(docFile, 'utf8');
-    const { frontmatter: fm } = extractFrontmatter(raw);
-    if (!fm || !fm.includes(basename)) continue;
+    if (!raw.includes(basename)) continue;
+    const { frontmatter: fm, body } = extractFrontmatter(raw);
+    if (!fm) continue;
 
     const docDir = path.dirname(docFile);
     const oldRelPath = path.relative(docDir, oldPath).split(path.sep).join('/');
-    if (fm.includes(oldRelPath) || fm.includes('./' + oldRelPath)) {
-      count++;
+    const fmHit = fm.includes(oldRelPath) || fm.includes('./' + oldRelPath);
+
+    let bodyHit = false;
+    if (!fmHit) {
+      const linkRegex = /\[[^\]]*\]\(([^)#]+\.md)(?:#[^)]*)?\)/g;
+      for (const match of body.matchAll(linkRegex)) {
+        const href = match[1];
+        if (/^https?:/i.test(href)) continue;
+        const docRelAbs = path.resolve(docDir, href);
+        const repoRelAbs = path.resolve(config.repoRoot, href);
+        if (docRelAbs === oldPath || repoRelAbs === oldPath) { bodyHit = true; break; }
+      }
     }
+
+    if (fmHit || bodyHit) count++;
   }
 
   return count;

package/src/render.mjs

@@ -377,7 +377,7 @@ export function renderCheck(index, config, opts = {}) {
 }
 
 function _renderCheck(index, opts = {}) {
-  const { errorsOnly, noCollapse } = opts;
+  const { errorsOnly, noCollapse, verbose } = opts;
   const lines = ['Check', ''];
   lines.push(`- docs scanned: ${index.docs.length}`);
   lines.push(`- errors: ${index.errors.length}`);
@@ -392,22 +392,32 @@ function _renderCheck(index, opts = {}) {
     lines.push('');
   }
 
+  // Warnings: terse by default — print count + pointer. The full per-doc list
+  // grew long enough on real projects that it drowned the summary; agents now
+  // see warnings as a single line and opt in to detail when they need it.
+  // --verbose / --no-collapse expand to the full list (with collapse-by-category
+  // still applied unless --no-collapse is set).
   if (!errorsOnly && index.warnings.length > 0) {
-    lines.push(yellow('Warnings'));
-    if (noCollapse) {
-      for (const issue of index.warnings) {
-        lines.push(`- ${issue.path}: ${issue.message}`);
+    if (verbose || noCollapse) {
+      lines.push(yellow('Warnings'));
+      if (noCollapse) {
+        for (const issue of index.warnings) {
+          lines.push(`- ${issue.path}: ${issue.message}`);
+        }
+      } else {
+        const { passthrough, collapsed } = categorizeWarnings(index.warnings);
+        for (const issue of passthrough) {
+          lines.push(`- ${issue.path}: ${issue.message}`);
+        }
+        for (const sum of collapsed) {
+          lines.push(`- ${sum.count} ${sum.label} — run \`${sum.fix}\` to bulk-fix`);
+        }
       }
+      lines.push('');
     } else {
-      const { passthrough, collapsed } = categorizeWarnings(index.warnings);
-      for (const issue of passthrough) {
-        lines.push(`- ${issue.path}: ${issue.message}`);
-      }
-      for (const sum of collapsed) {
-        lines.push(`- ${sum.count} ${sum.label} — run \`${sum.fix}\` to bulk-fix`);
-      }
+      lines.push(dim(`Run \`dotmd check --verbose\` for per-doc detail, or \`dotmd doctor\` to auto-fix where possible.`));
+      lines.push('');
     }
-    lines.push('');
   }
 
   if (index.errors.length === 0 && index.warnings.length === 0) {