• mermaid (mmdc): /usr/local/bin/mmdc is a broken symlink (dangling reference to a removed node_modules path). Works via npx with PUPPETEER_EXECUTABLE_PATH=/usr/local/bin/chrome and PUPPETEER_SKIP_DOWNLOAD=1, but npx is slow (~5s per diagram) and unreliable for batch publish. ob-mermaid is configured in project-config.el for interactive use (C-c C-c) but not batch.
• ditaa: requires AWT (Java GUI subsystem). GraalVM JDK 21 on this host is missing libXext.so.6. Would work with OpenJDK + X11 libs installed.
• gnuplot: ob-gnuplot fails silently in batch. Likely a terminal configuration issue (set terminal png before set output).
• plantuml: same AWT dependency as ditaa (both are Java). Broken until libXext is installed.

The project-config.el comment "FreeBSD lacks puppeteer support" (added ~2025) was partially wrong. FreeBSD 15 has Chromium 143 installed. Puppeteer works at runtime when told to use system Chromium via PUPPETEER_EXECUTABLE_PATH. The failure is in puppeteer's postinstall script, which tries to download a Chromium binary (no FreeBSD build exists). Fix: PUPPETEER_SKIP_DOWNLOAD=1 npm install -g @mermaid-js/mermaid-cli.

The practical decision: use graphviz for all diagrams in the publish pipeline. Mermaid is available for interactive use but not reliable for batch. The graphviz suite (dot, neato, fdp, sfdp, twopi, circo) is native, fast, and fully supported.

digraph G {
    rankdir=LR;
    node [shape=box, style="rounded,filled", fillcolor="#f5f5f5"];
    A [label="Source"];
    B [label="Process"];
    C [label="Output"];
    A -> B -> C;
}

This block:

• Renders inline when you press C-c C-c in Emacs.
• Generates diagram-test-dot.png in the same directory as the org file.
• Embeds the image in the exported HTML when gmake publish runs.
• No manual steps. No pre-committed PNGs. No Makefile target.

digraph G {
    rankdir=TB;
    node [shape=box];
    "org file" -> "C-c C-v t" -> ".dot file";
    "org file" -> "C-c C-c" -> ".png file";
    "org file" -> "gmake publish" -> ".html + .png";
}

:tangle writes the .dot source to disk when you invoke C-c C-v t. Useful when you want to edit the diagram with a graphviz-specific tool (xdot, dot -Tx11, an IDE plugin).

All graphviz engines use the same DOT language but different layout algorithms:

Usage:

graph G {
    A -- B -- C -- D -- A;
    A -- C;
    B -- D;
}

:file extension determines format: .png, .svg, .pdf. SVG is preferable for web (scalable, smaller), but org-publish's wal.sh-research-images component handles all three:

:base-extension "png\\|jpg\\|gif\\|svg\\|pdf\\|pptx"

Convert mermaid → dot where the diagram matters for the published site. Leave mermaid blocks as-is where they're purely notes (never published, or published as code blocks rather than images).

Most of the 55 blocks are flowcharts and sequence diagrams. Flowcharts convert directly; sequence diagrams approximate with numbered edges (as in the egress-proxy diagram).