fix: prevent rename from corrupting overlapping entity ids

skills/story-maintenance/scripts/story.js

@@ -77,6 +77,11 @@ function parseYaml(source) {
       continue;
     }
     const parsed = parseArray(lines, index + 1);
+    if (parsed.nextIndex === index + 1) {
+      data[key] = "";
+      index += 1;
+      continue;
+    }
     data[key] = parsed.items;
     index = parsed.nextIndex;
   }
@@ -1643,9 +1648,10 @@ function ensureFile(filePath, contents, changed, root) {
   assertSafeProjectPath(filePath, root);
 }
 function replaceEntityReferences(root, oldId, newId) {
+  const pattern = new RegExp(`(?<![a-z0-9-])${escapeRegExp(oldId)}(?![a-z0-9-])`, "g");
   for (const file of markdownFiles(root)) {
     const text = safeRead(file, root);
-    const updated = text.replaceAll(oldId, newId);
+    const updated = text.replace(pattern, newId);
     if (updated !== text) {
       writeFile(file, updated, { root });
     }
@@ -1658,7 +1664,9 @@ function removeEntityReferences(root, id) {
     }
     const markdown = readMarkdown(file, root);
     const data = removeReferenceFromData(markdown.data, id);
-    writeFile(file, replaceFrontmatter(markdown.rawMarkdown, data), { root });
+    if (JSON.stringify(data) !== JSON.stringify(markdown.data)) {
+      writeFile(file, replaceFrontmatter(markdown.rawMarkdown, data), { root });
+    }
   }
 }
 function applyEntityBacklinks(root, kind, id, data) {
@@ -1753,10 +1761,11 @@ function writeEpub(outFile, storyId, manuscript, writeOptions = {}) {
     chapterItems.push(`<item id="${id}" href="${id}.xhtml" media-type="application/xhtml+xml"/>`);
     spineItems.push(`<itemref idref="${id}"/>`);
   }
+  const modified = new Date().toISOString().replace(/\.\d{3}Z$/, "Z");
   writeZip(outFile, [
     { name: "mimetype", content: "application/epub+zip" },
     { name: "META-INF/container.xml", content: `<?xml version="1.0" encoding="UTF-8"?><container version="1.0" xmlns="urn:oasis:names:tc:opendocument:xmlns:container"><rootfiles><rootfile full-path="OEBPS/content.opf" media-type="application/oebps-package+xml"/></rootfiles></container>` },
-    { name: "OEBPS/content.opf", content: `<?xml version="1.0" encoding="UTF-8"?><package version="3.0" unique-identifier="book-id" xmlns="http://www.idpf.org/2007/opf"><metadata xmlns:dc="http://purl.org/dc/elements/1.1/"><dc:identifier id="book-id">${xmlEscape(storyId)}</dc:identifier><dc:title>${xmlEscape(manuscript.title)}</dc:title><dc:language>en</dc:language></metadata><manifest><item id="nav" href="nav.xhtml" media-type="application/xhtml+xml" properties="nav"/>${chapterItems.join("")}</manifest><spine>${spineItems.join("")}</spine></package>` },
+    { name: "OEBPS/content.opf", content: `<?xml version="1.0" encoding="UTF-8"?><package version="3.0" unique-identifier="book-id" xmlns="http://www.idpf.org/2007/opf"><metadata xmlns:dc="http://purl.org/dc/elements/1.1/"><dc:identifier id="book-id">${xmlEscape(storyId)}</dc:identifier><dc:title>${xmlEscape(manuscript.title)}</dc:title><dc:language>en</dc:language><meta property="dcterms:modified">${modified}</meta></metadata><manifest><item id="nav" href="nav.xhtml" media-type="application/xhtml+xml" properties="nav"/>${chapterItems.join("")}</manifest><spine>${spineItems.join("")}</spine></package>` },
     { name: "OEBPS/nav.xhtml", content: navXhtml(manuscript) },
     ...chapterEntries
   ], writeOptions);
@@ -1785,8 +1794,10 @@ function writeDocx(outFile, manuscript, writeOptions = {}) {
   }
   const body = bodyParts.join("");
   writeZip(outFile, [
-    { name: "[Content_Types].xml", content: `<?xml version="1.0" encoding="UTF-8"?><Types xmlns="http://schemas.openxmlformats.org/package/2006/content-types"><Default Extension="rels" ContentType="application/vnd.openxmlformats-package.relationships+xml"/><Default Extension="xml" ContentType="application/xml"/><Override PartName="/word/document.xml" ContentType="application/vnd.openxmlformats-officedocument.wordprocessingml.document.main+xml"/></Types>` },
+    { name: "[Content_Types].xml", content: `<?xml version="1.0" encoding="UTF-8"?><Types xmlns="http://schemas.openxmlformats.org/package/2006/content-types"><Default Extension="rels" ContentType="application/vnd.openxmlformats-package.relationships+xml"/><Default Extension="xml" ContentType="application/xml"/><Override PartName="/word/document.xml" ContentType="application/vnd.openxmlformats-officedocument.wordprocessingml.document.main+xml"/><Override PartName="/word/styles.xml" ContentType="application/vnd.openxmlformats-officedocument.wordprocessingml.styles+xml"/></Types>` },
     { name: "_rels/.rels", content: `<?xml version="1.0" encoding="UTF-8"?><Relationships xmlns="http://schemas.openxmlformats.org/package/2006/relationships"><Relationship Id="rId1" Type="http://schemas.openxmlformats.org/officeDocument/2006/relationships/officeDocument" Target="word/document.xml"/></Relationships>` },
+    { name: "word/_rels/document.xml.rels", content: `<?xml version="1.0" encoding="UTF-8"?><Relationships xmlns="http://schemas.openxmlformats.org/package/2006/relationships"><Relationship Id="rId1" Type="http://schemas.openxmlformats.org/officeDocument/2006/relationships/styles" Target="styles.xml"/></Relationships>` },
+    { name: "word/styles.xml", content: `<?xml version="1.0" encoding="UTF-8"?><w:styles xmlns:w="http://schemas.openxmlformats.org/wordprocessingml/2006/main"><w:style w:type="paragraph" w:styleId="Title"><w:name w:val="Title"/><w:pPr><w:spacing w:after="240"/><w:jc w:val="center"/></w:pPr><w:rPr><w:b/><w:sz w:val="56"/></w:rPr></w:style><w:style w:type="paragraph" w:styleId="Heading1"><w:name w:val="heading 1"/><w:pPr><w:spacing w:before="480" w:after="240"/></w:pPr><w:rPr><w:b/><w:sz w:val="32"/></w:rPr></w:style></w:styles>` },
     { name: "word/document.xml", content: `<?xml version="1.0" encoding="UTF-8"?><w:document xmlns:w="http://schemas.openxmlformats.org/wordprocessingml/2006/main"><w:body>${body}<w:sectPr/></w:body></w:document>` }
   ], writeOptions);
 }
@@ -2418,6 +2429,8 @@ Options:
   --category <name>         Category for add term
   --alias <name>            Alias for add term; repeatable
   -h, --help                Show this help
+
+Option values that begin with a dash must use the --option=value form.
 `;
 function runCli(argv, io) {
   const parsed = parseArgs(argv);

src/cli.js

@@ -72,6 +72,8 @@ Options:
   --category <name>         Category for add term
   --alias <name>            Alias for add term; repeatable
   -h, --help                Show this help
+
+Option values that begin with a dash must use the --option=value form.
 `;
 
 export function runCli(argv, io) {

src/frontmatter.js

@@ -78,6 +78,12 @@ function parseYaml(source) {
     }
 
     const parsed = parseArray(lines, index + 1);
+    if (parsed.nextIndex === index + 1) {
+      data[key] = "";
+      index += 1;
+      continue;
+    }
+
     data[key] = parsed.items;
     index = parsed.nextIndex;
   }

src/markdown.js

@@ -57,7 +57,7 @@ export function extractSection(markdown, heading) {
   return (next ? rest.slice(0, next.index) : rest).trim();
 }
 
-function escapeRegExp(value) {
+export function escapeRegExp(value) {
   return value.replace(/[.*+?^${}()|[\]\\]/g, "\\$&");
 }
 

src/story.js

@@ -2,7 +2,7 @@ import { Buffer } from "node:buffer";
 import fs from "node:fs";
 import path from "node:path";
 import { parseFrontmatter, replaceFrontmatter, stringifyFrontmatter } from "./frontmatter.js";
-import { chapterProse, extractSection, kebabCase, titleCaseSlug, wordCount } from "./markdown.js";
+import { chapterProse, escapeRegExp, extractSection, kebabCase, titleCaseSlug, wordCount } from "./markdown.js";
 
 export const STORY_SCHEMA_VERSION = 2;
 
@@ -1615,9 +1615,12 @@ function ensureFile(filePath, contents, changed, root) {
 }
 
 function replaceEntityReferences(root, oldId, newId) {
+  // Only replace whole ids: an id can be a substring of another id or of a
+  // prose word, so matches adjacent to id characters must be left alone.
+  const pattern = new RegExp(`(?<![a-z0-9-])${escapeRegExp(oldId)}(?![a-z0-9-])`, "g");
   for (const file of markdownFiles(root)) {
     const text = safeRead(file, root);
-    const updated = text.replaceAll(oldId, newId);
+    const updated = text.replace(pattern, newId);
     if (updated !== text) {
       writeFile(file, updated, { root });
     }
@@ -1631,7 +1634,9 @@ function removeEntityReferences(root, id) {
     }
     const markdown = readMarkdown(file, root);
     const data = removeReferenceFromData(markdown.data, id);
-    writeFile(file, replaceFrontmatter(markdown.rawMarkdown, data), { root });
+    if (JSON.stringify(data) !== JSON.stringify(markdown.data)) {
+      writeFile(file, replaceFrontmatter(markdown.rawMarkdown, data), { root });
+    }
   }
 }
 
@@ -1737,10 +1742,11 @@ function writeEpub(outFile, storyId, manuscript, writeOptions = {}) {
     spineItems.push(`<itemref idref="${id}"/>`);
   }
 
+  const modified = new Date().toISOString().replace(/\.\d{3}Z$/, "Z");
   writeZip(outFile, [
     { name: "mimetype", content: "application/epub+zip" },
     { name: "META-INF/container.xml", content: `<?xml version="1.0" encoding="UTF-8"?><container version="1.0" xmlns="urn:oasis:names:tc:opendocument:xmlns:container"><rootfiles><rootfile full-path="OEBPS/content.opf" media-type="application/oebps-package+xml"/></rootfiles></container>` },
-    { name: "OEBPS/content.opf", content: `<?xml version="1.0" encoding="UTF-8"?><package version="3.0" unique-identifier="book-id" xmlns="http://www.idpf.org/2007/opf"><metadata xmlns:dc="http://purl.org/dc/elements/1.1/"><dc:identifier id="book-id">${xmlEscape(storyId)}</dc:identifier><dc:title>${xmlEscape(manuscript.title)}</dc:title><dc:language>en</dc:language></metadata><manifest><item id="nav" href="nav.xhtml" media-type="application/xhtml+xml" properties="nav"/>${chapterItems.join("")}</manifest><spine>${spineItems.join("")}</spine></package>` },
+    { name: "OEBPS/content.opf", content: `<?xml version="1.0" encoding="UTF-8"?><package version="3.0" unique-identifier="book-id" xmlns="http://www.idpf.org/2007/opf"><metadata xmlns:dc="http://purl.org/dc/elements/1.1/"><dc:identifier id="book-id">${xmlEscape(storyId)}</dc:identifier><dc:title>${xmlEscape(manuscript.title)}</dc:title><dc:language>en</dc:language><meta property="dcterms:modified">${modified}</meta></metadata><manifest><item id="nav" href="nav.xhtml" media-type="application/xhtml+xml" properties="nav"/>${chapterItems.join("")}</manifest><spine>${spineItems.join("")}</spine></package>` },
     { name: "OEBPS/nav.xhtml", content: navXhtml(manuscript) },
     ...chapterEntries
   ], writeOptions);
@@ -1773,8 +1779,10 @@ function writeDocx(outFile, manuscript, writeOptions = {}) {
   const body = bodyParts.join("");
 
   writeZip(outFile, [
-    { name: "[Content_Types].xml", content: `<?xml version="1.0" encoding="UTF-8"?><Types xmlns="http://schemas.openxmlformats.org/package/2006/content-types"><Default Extension="rels" ContentType="application/vnd.openxmlformats-package.relationships+xml"/><Default Extension="xml" ContentType="application/xml"/><Override PartName="/word/document.xml" ContentType="application/vnd.openxmlformats-officedocument.wordprocessingml.document.main+xml"/></Types>` },
+    { name: "[Content_Types].xml", content: `<?xml version="1.0" encoding="UTF-8"?><Types xmlns="http://schemas.openxmlformats.org/package/2006/content-types"><Default Extension="rels" ContentType="application/vnd.openxmlformats-package.relationships+xml"/><Default Extension="xml" ContentType="application/xml"/><Override PartName="/word/document.xml" ContentType="application/vnd.openxmlformats-officedocument.wordprocessingml.document.main+xml"/><Override PartName="/word/styles.xml" ContentType="application/vnd.openxmlformats-officedocument.wordprocessingml.styles+xml"/></Types>` },
     { name: "_rels/.rels", content: `<?xml version="1.0" encoding="UTF-8"?><Relationships xmlns="http://schemas.openxmlformats.org/package/2006/relationships"><Relationship Id="rId1" Type="http://schemas.openxmlformats.org/officeDocument/2006/relationships/officeDocument" Target="word/document.xml"/></Relationships>` },
+    { name: "word/_rels/document.xml.rels", content: `<?xml version="1.0" encoding="UTF-8"?><Relationships xmlns="http://schemas.openxmlformats.org/package/2006/relationships"><Relationship Id="rId1" Type="http://schemas.openxmlformats.org/officeDocument/2006/relationships/styles" Target="styles.xml"/></Relationships>` },
+    { name: "word/styles.xml", content: `<?xml version="1.0" encoding="UTF-8"?><w:styles xmlns:w="http://schemas.openxmlformats.org/wordprocessingml/2006/main"><w:style w:type="paragraph" w:styleId="Title"><w:name w:val="Title"/><w:pPr><w:spacing w:after="240"/><w:jc w:val="center"/></w:pPr><w:rPr><w:b/><w:sz w:val="56"/></w:rPr></w:style><w:style w:type="paragraph" w:styleId="Heading1"><w:name w:val="heading 1"/><w:pPr><w:spacing w:before="480" w:after="240"/></w:pPr><w:rPr><w:b/><w:sz w:val="32"/></w:rPr></w:style></w:styles>` },
     { name: "word/document.xml", content: `<?xml version="1.0" encoding="UTF-8"?><w:document xmlns:w="http://schemas.openxmlformats.org/wordprocessingml/2006/main"><w:body>${body}<w:sectPr/></w:body></w:document>` }
   ], writeOptions);
 }

test/frontmatter.test.js

@@ -29,6 +29,17 @@ Body`);
     expect(parsed.raw).toContain("name:");
   });
 
+  test("parses bare keys with no value as empty strings", () => {
+    const parsed = parseFrontmatter(`---
+introduced:
+aliases: []
+resolved:
+---
+Body`);
+
+    expect(parsed.data).toEqual({ introduced: "", aliases: [], resolved: "" });
+  });
+
   test("stringifies and replaces frontmatter", () => {
     const yaml = stringifyFrontmatter({
       title: "The Last Ember",

test/story.test.js

@@ -642,6 +642,40 @@ word-count: 1
     expect(scanProject(created.root).story.data["schema-version"]).toBe(STORY_SCHEMA_VERSION);
   });
 
+  test("remove scrubs references without rewriting untouched files", () => {
+    const cwd = makeTempDir();
+    const created = createStoryProject({ cwd, title: "Remove Touch", force: false });
+    createEntity(created.root, { kind: "character", name: "Keeper", role: "supporting" });
+    createEntity(created.root, { kind: "promise", name: "Old Setup", character: "keeper" });
+    const storyPath = path.join(created.root, "story.md");
+    fs.writeFileSync(storyPath, fs.readFileSync(storyPath, "utf8").replace("title:", "# hand-written note\ntitle:"), "utf8");
+    const annotated = fs.readFileSync(storyPath, "utf8");
+
+    removeEntity(created.root, { kind: "character", id: "keeper" });
+
+    expect(fs.readFileSync(storyPath, "utf8")).toBe(annotated);
+    expect(fs.readFileSync(path.join(created.root, "continuity", "promises", "old-setup.md"), "utf8")).not.toContain("keeper");
+  });
+
+  test("rename leaves overlapping entity ids and prose words intact", () => {
+    const cwd = makeTempDir();
+    const created = createStoryProject({ cwd, title: "Rename Overlap", force: false });
+    createEntity(created.root, { kind: "character", name: "Mara", role: "protagonist" });
+    createEntity(created.root, { kind: "character", name: "Mara Quill", role: "supporting" });
+    createEntity(created.root, { kind: "chapter", name: "Arrival", number: 1, pov: "mara-quill", character: "mara-quill,mara" });
+    const chapterPath = path.join(created.root, "chapters", "chapter-01.md");
+    fs.appendFileSync(chapterPath, "The marathon passed mara on the docks.\n", "utf8");
+
+    renameEntity(created.root, { kind: "character", id: "mara", name: "Tess" });
+
+    const chapterText = fs.readFileSync(chapterPath, "utf8");
+    expect(chapterText).toContain("pov: mara-quill");
+    expect(chapterText).toContain("- tess");
+    expect(chapterText).toContain("The marathon passed tess on the docks.");
+    expect(fs.existsSync(path.join(created.root, "characters", "mara-quill.md"))).toBe(true);
+    expect(validateLinks(created.root)).toEqual({ ok: true, errors: [], warnings: [] });
+  });
+
   test("covers helper errors, fallback branches, and malformed continuity state", () => {
     const cwd = makeTempDir();
     const created = createStoryProject({ cwd, title: "Coverage Branches", force: false });
@@ -818,7 +852,9 @@ word-count: 0
       format: "docx"
     });
     expect(fs.readFileSync(epub.outFile).readUInt32LE(0)).toBe(0x04034b50);
+    expect(fs.readFileSync(epub.outFile).toString("utf8")).toContain("dcterms:modified");
     expect(fs.readFileSync(docx.outFile).toString("utf8")).toContain("word/document.xml");
+    expect(fs.readFileSync(docx.outFile).toString("utf8")).toContain("word/styles.xml");
     expect(() => buildBook(created.root, { format: "pdf" })).toThrow("Unsupported build format: pdf");
   });
 });