U-Mentalism — Research Notebook

Operational manual for the notebook hosted at www.u-mentalism.com.

Maintained as an independent research project by Luís Homem, PhD (ORCID 0000-0003-3520-1489).

For the project's identification and scope, see the live site. This file documents how the notebook is built, configured, stored, and synced — material that previously lived in the in-site About panel and was moved here so the About could keep an institutional shape.

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How storage works

Reflections live in your browser's localStorage. PDF URLs are also stored there. Nothing is sent anywhere — everything stays on your device. To move data between machines, use Export / Import.

PDFs & Repository at the top of each tab

Each tab can display one or more PDFs (configured by DOI or URL) and link to a GitHub repository or directory. The author hosts each document (Common Ground, own server, arXiv, Drive direct-link, etc.) and pastes its DOI via Set source. The site accepts:

• A bare DOI: 10.XXXX/XXXXX
• A resolved DOI URL: https://doi.org/10.XXXX/XXXXX
• Any direct PDF URL
• An optional GitHub URL pointing to a repository, file, or directory (shows as ↗ Code)

When two or more documents are attached to the same tab, a chip strip appears above the viewer; click a chip to switch the active document, or click the × on a chip to remove it. Visitors read the active document inline and use ↓ Download to retrieve a copy. When a DOI is given, it is shown in the status line and resolves via doi.org.

GitHub

The site footer links to github.com/U-Mentalism. Per-tab repository links can point to any path within any repo there (e.g. /U-Mentalism/assembly, /U-Mentalism/blockchain, etc.). The notebook itself is hosted as a static file inside U-Mentalism/U-Mentalism.github.io via GitHub Pages.

GitHub Sync (optional)

Reflections can be committed automatically to a chosen repo via the ⚙ Sync button in the sidebar. Single-author setup using a fine-grained Personal Access Token scoped to a single repo, with Contents: Read and write only. Each tab is stored as reflections/NN.md; auto-push commits when the editor loses focus or the browser tab becomes hidden — one commit per writing burst, not per keystroke. Manual Push all / Pull all are available in the Sync modal at any time. The notebook works offline either way; sync just keeps a Git-versioned mirror.

The token is kept in the browser's localStorage. Revoke it from GitHub at any time. Single-user use only.

Repository layout

The notebook expects (and will create) this structure on first push:

{repo}/
├── reflections/
│   ├── 01.md   ← Philosophia Naturalis / Artificialis
│   ├── 02.md   ← Computer Architecture & Photonics
│   ├── 03.md   ← Universal Assembly Language
│   ├── 04.md   ← Blockchain Economy
│   ├── 05.md   ← Cities & Energy
│   ├── 06.md   ← Ethics & Neuroscience
│   ├── 07.md   ← Enlightenment / Cybernetica
│   └── 08.md   ← Indice / Codex
└── (anything else you keep in the repo: site, docs, code, etc.)

Markdown & LaTeX

Use standard Markdown for structure. Use $...$ for inline math and $$...$$ for display math. The in-browser engine is KaTeX — fast, but math-only (no \usepackage, no TikZ, no full LaTeX). Examples:

• $E = mc^2$ renders inline
• $$\int_0^\infty e^{-x^2}\,dx = \frac{\sqrt{\pi}}{2}$$ renders centered

Full LaTeX via Overleaf

For real LaTeX with packages (TikZ, biblatex, etc.), each tab has an ↗ Overleaf button. It converts the section to a complete .tex document with a standard preamble (amsmath, amssymb, mathtools, graphicx, hyperref, geometry, microtype, enumitem) and posts it to Overleaf, opening a new project pre-filled. From there, add any \usepackage{...} you need.

Markdown→LaTeX conversion is approximate; review plain-text paragraphs for stray characters and clean up in Overleaf as needed.

Operational note — log in to Overleaf first

The button submits a POST to https://www.overleaf.com/docs with the converted .tex as the request body. If you are not logged in to Overleaf when you click, Overleaf intercepts the request with a login redirect, and the body of the original POST is lost in the round-trip. The result is a project that is created but inconsistent — typically with the title preserved (taken from \title{} before the redirect consumed the body) but with body content missing or unrelated.

Always make sure you are logged in to Overleaf in the same browser session before clicking ↗ Overleaf. Open overleaf.com in another tab, confirm you are logged in, then click the button. The new tab will open the project directly without an auth detour.

Known limitations of the Markdown→LaTeX converter

The converter is a bridge for Markdown + LaTeX math, not a full Markdown implementation. The following Markdown constructs are not supported and either render as literal text or render in a degraded way. For any of these, write your Markdown in the editor for the parts the converter handles, click ↗ Overleaf, and finish in Overleaf using full LaTeX:

• Tables. Markdown table syntax (| col1 | col2 |, etc.) is not parsed — the lines render as plain text with the pipes preserved. Use LaTeX tabular or array directly in Overleaf.
• Images. ![alt](url) is not handled as an image — the leading ! falls outside the link regex, so it appears literally and the rest is captured as a regular hyperlink. Use \includegraphics in Overleaf.
• Inline HTML. Tags like <strong>, <em>, <br> are not interpreted — they render as literal text ([T1]{fontenc} makes < and > print correctly).
• URLs containing parentheses. The link regex captures up to the first ), so [text](https://example.com/path(with)parens) truncates the URL at the inner ) and leaves the rest as trailing text. Escape the parentheses in the URL or use \href in Overleaf.
• Raw LaTeX commands outside math. Anything like \textbf{...}, \section{...}, \begin{...} typed directly in the editor (outside $...$ or $$...$$) is treated as plain text and escaped — \textbf{x} renders literally, not as bold. The bridge only passes LaTeX through inside math delimiters. For prose-level LaTeX, write Markdown in the editor and finish in Overleaf.
• Nested lists. Only top-level bullets (- item at column 0) and top-level enumerations (1. item) are recognised. Indented children ( - child) fall through as plain text. Use LaTeX itemize/enumerate nesting in Overleaf.
• Adjacent mixed lists. A bulleted list immediately followed by an enumerated list (no blank line between) renders as two separate environments adjacent without explicit visual separation.

What is supported and converts cleanly: headings (# to #### → \section / \subsection / \subsubsection / \paragraph), bold (**...**), italic (*...*), inline code (`...`), fenced code blocks (```lang), links ([text](url)) where the URL has no inner parentheses, top-level itemize and enumerate lists, blockquotes, horizontal rules (--- on its own line), inline math ($...$), display math ($$...$$), Markdown-escaped dollar signs (\$ → literal $), all Latin special characters via the [T1]{fontenc} preamble, and the standard escaped specials (& % _ # ^ ~ \ { }) inside paragraph text.

Recommended workflow

• Publish papers on Common Ground (or arXiv, Zenodo, etc.) and copy the DOI.
• Paste the DOI(s) per tab via Set source — multiple documents can be added to the same tab.
• Write reflections, paste AI critiques, develop ideas in the editor below.
• Export periodically as a JSON backup.