To set EPUB page order, define the reading sequence in the package document’s spine: title, in-book table of contents, body, then colophon. Do not infer that sequence from the number of table-of-contents links. In the sample for this article, three body chapters and one colophon source produced a seven-resource spine: title.xhtml, nav.xhtml, p001.xhtml through p004.xhtml, and colophon.xhtml. This article tests the order reached by moving forward through the book, not the difference between an in-book TOC and a device menu.
Answer: Use the spine to judge page order
An EPUB contains both a list of links that readers can choose and a reading order used for sequential navigation. The EPUB navigation document supplies the links, while the package document’s spine supplies the reading order. A TOC with three entries therefore does not prove that the title page and colophon occupy the intended positions.
A product-independent workflow starts by assigning every source one role: title, TOC, body, or colophon. Next, fix the chapter order and decide which sources belong in navigation. Finally, compare the generated spine and navigation targets separately. Keep the source settings authoritative; editing generated XHTML to force a new order makes the next build difficult to reproduce.
Sample: Separate five roles across three body chapters
The article-specific sample used the title “五区分順序 STUDIO-430,” author “Rune Verification,” publisher “Evidence Press,” horizontal Japanese layout, volume 0, version 1.0, and publication date 2026-08-31. Its inputs were three body files, numbered 01 through 03, plus 99-colophon. No cover image was supplied.
The five conceptual roles are title, in-book TOC, body, colophon input, and generated colophon. They do not map one-to-one to five files because the body consists of three chapters. The expected generated spine therefore contains seven resources. Counting roles as files would make a correct multi-chapter body look like duplication.
The starting configuration set title position 0 and TOC position 1. Input 4, 99-colophon, was excluded from navigation. The expected TOC contained only the three body chapters. The lack of a cover was also part of the baseline, so an image count of zero is not a missing asset in this test.
Operation: Fix chapter order and navigation inclusion before export
In a product-independent process, number the manuscript files, mark supplementary pages that should not appear in navigation, and record the intended role of every source. After export, inspect the spine for reading order, nav.xhtml for EPUB 3 navigation, and NCX for legacy navigation. If one list is wrong, return to chapter order or navigation inclusion instead of patching the generated package.
For the Rune Studio run, the work metadata and version were set first. The three body files and 99-colophon were then selected. The plan used title position 0, TOC position 1, and navigation exclusion for input 4. After reviewing that plan, the workflow ran export and inspect, then read the package spine, nav.xhtml, NCX, and missing-resource result separately.
Excluding the colophon source from navigation did not remove it from reading order. The run retained that source as p004.xhtml and also generated colophon.xhtml after it. “Not listed in the TOC” and “not included in the book” are different decisions.
Measurement: Seven spine resources and three navigation entries
The article-specific Stage 4 record has status=passed and command_count=9. Local inspection returned valid=true, spine_count=7, image_count=0, missing_images=0, has_nav=true, and has_ncx=true. The observed spine was title.xhtml, nav.xhtml, p001.xhtml, p002.xhtml, p003.xhtml, p004.xhtml, and colophon.xhtml.
Both navigation formats contained three entries. The nav targets were p001.xhtml, p002.xhtml, and p003.xhtml; the NCX targets were Text/p001.xhtml, Text/p002.xhtml, and Text/p003.xhtml. The three body chapters were listed, while the fourth input remained in the reading order without becoming a navigation item. The result also recorded body_chapters=3 and colophon_position=4.
Although the command supplied title position 0 and TOC position 1, the compact article-specific result recorded title_position=null and toc_position=null. The observed spine proves that the title and nav came first in this export, but the null summary values do not prove that those settings were retained for later reuse. A workflow that needs reusable position metadata should return to the saved plan or configuration record.
A separate common Stage 4 run used four chapters, horizontal layout, version 1.0, and produced spine=8, one image, no missing images, nav and NCX present, and valid=true in nine commands. That result exercises the shared generation path; it does not replace this article’s cover-free, three-chapter sample.
Limits: Local order does not establish retailer or device behavior
Here, valid=true is limited to a local structural inspection of an EPUB built from a dedicated copy. KDP submission and review, retailer conversion, Kindle Previewer, hardware page turns, and matching presentation across all readers were not tested. The zero image count belongs only to the no-cover baseline and cannot support a claim about a covered EPUB.
Use the symptom to choose a return point. If the title or TOC is not first, return to position settings and the export plan. If the three chapters are out of order, return to the source list. If the colophon appears in navigation, return to input 4’s navigation setting. If a spine resource is absent, return to source selection and the export log. If explicit title or TOC position values are required but remain null, capture the configuration again rather than inferring it from display order.
Rune Studio’s role: Generate EPUB 3 structure from source settings
The EPUB 3.3 specification assigns distinct roles to the package manifest and spine and to the EPUB navigation document. That is an industry-standard distinction, not a claim about a particular application’s interface or retailer acceptance.
Rune Studio’s documented Mac workflow uses an EPUB Wizard to set work information, volume, manuscript files, chapter order, TOC inclusion, cover, and publication date. It can generate EPUB 3 content including body XHTML, title, TOC, colophon, nav.xhtml, legacy-compatible NCX, and a content.opf package. The Stage 4 numbers above are local measurements of one generated package, kept separate from those documented product capabilities. Current product information is available on the Rune Studio product page.
Conclusion: Reconcile seven spine resources by role
For EPUB page order, inspect the spine before treating TOC counts as evidence. In this cover-free sample, seven resources represented the title, nav, three body chapters, colophon input, and generated colophon, while navigation contained only the three body chapters. Counting roles, spine resources, and navigation entries separately exposes a missing input without misclassifying an intentional exclusion.
Before applying the setup to a production manuscript, verify the seven-item spine, the three matching nav and NCX targets, and zero missing resources in the same build. This article ends at whole-book reading order; it does not use that result to settle how an in-book TOC differs from a device menu.
