Automating Jekyll Site Generation: From NavGraph to Navigable Hubs

This entry documents a pivotal moment of translating theoretical information architecture into practical web development. My excitement is palpable as I see the ‘Rule of 7’ come to life, guiding the automated creation of a Jekyll site. The iterative problem-solving, from initial Python script to debugging Jekyll’s nuances and refining the user experience, perfectly encapsulates the hands-on methodology I champion. It’s about building a ‘Forever Machine’ with an interface that truly reflects its underlying structure.

By Mike Levin

Monday, December 15, 2025

Get Pipulate [View Markdown Source]

Setting the Stage: Context for the Curious Book Reader

In the ongoing quest to construct a resilient and intuitively navigable digital knowledge base, this entry chronicles an interesting step in materializing abstract graph data into a concrete, interactive website structure. It details the iterative process of programmatically generating Jekyll hub pages from a navgraph.json blueprint, addressing technical hurdles, and refining the site’s information architecture for both human and AI consumption. This foundational work is important to know in the Age of AI, as it directly impacts how our digital artifacts are understood and traversed.

Technical Journal Entry Begins

Alright, it should now “be easy” to write out the hub pages and make the site fully drill-down-able using navgraph.json. I guess it would be yet another .py file, let’s keep it still in the d3js folder for now for consistency. I’ll probably organize the folder names layer to give some sub-section of the Pipulate project a real Jekyll/headless Shopify flair. If you’re on Shopify you might as well go headless for 100% control and if you’re using the Liquid Template system for Shopify even when headless then you might as well also lean into the Jekyll static site generator for both creating the static headless site (yes, that should be possible) and managing the blog.

This work here optimizes the blog surface area for search and the user/AI surfing experience, leading into small-world-theory to get every page reachable quick. There will almost certainly be way more fine-grained granular fine-tuning about the decisions going into load-balancing those pages according to the Rule of 7 because right now it’s probably purely statistical and thresholds. There is inevitably “near duplicate” issues and “why here and not there” questions lurking in the work I’ve done so far. Making it real (this step) will surface those issues. Better here than on a client site. But I will always be able to point to this as a self-describing example of the issues.

The NavGraph Blueprint: Laying the Foundation

Alright, enough talk as the AI keeps telling me. I love to type. We Enjoy Tying. WET! Okay, let’s get to work. What are we doing here, Gemini? Stepping through navgraph.json I presume, making 1 page per container node while avoiding collisions. We don’t have to do it all in this one step. Work at the higher levels and work your way down to the granular details using as many stop-points in your responses as you feel necessary for us to bank a small win, do a git commit, make any small directional adjustments, and continue our way forward. For example, we can avoid the fact that there’s articles listed in each of these containers on the first pass so you can concentrate on the skeletal drill-down experience.

We can go so far as to say that the first implementation won’t even be in /home/mike/repos/MikeLev.in/ but rather in /home/mike/repos/trimnoir/ which I believe you’ve seen the config and IaC Nix flake for. I haven’t even put a homepage or default layout there. It’s a complete blank slate. We can write into the website repo’s root /home/mike/repos/trimnoir/ if you think it’s best for a system like this, or we can write into a subfolder named whatever you think is most appropriate in this case to keep the repo root clean.

Oh and within that subfolder you have the choice of nesting folders to represent hierarchy, but I don’t like changing directories much and I think this system is naturally bounded so besides the one folder you make for all the hub pages, maybe inside of there we should keep it flat and use the permalink of the YAML frontmatter to create idealized “virtual paths” in the URL that reflect the drill-down, though admittedly if we don’t change URLs of the landing pages that final click on the article will “pop it out of” the directory it feels like they were drilling down to. But that’s fine for first pass. We may or may not fix that depending, so we’ll cross each bridge as we come to them.

Let’s cross the page-generation bridge now, please and thank you.

Phase 1: Pouring the Concrete Skeleton

Gemini: This is the “Pouring Concrete” phase. We are taking the abstract blueprint (navgraph.json) and materializing it into real files that a web server can render.

We will start with Phase 1: The Skeleton.

We will focus purely on generating the Hub Pages and linking them to their child hubs. We will ignore the articles for a moment to ensure the “drill-down” logic holds water. We will target your sandbox repo (trimnoir) to keep things safe and clean.

The Strategy: Flat Files, Virtual Paths

Target: /home/mike/repos/trimnoir/_hubs/ (New directory to keep root clean).
Naming: hub_SLUG.md (e.g., hub_python.md). Flat structure on disk.
Routing: The permalink: /python/ in the YAML frontmatter handles the URL structure. Jekyll doesn’t care where the file lives; it only cares what the permalink says.
Layout: We’ll assume a standard layout (page or a new hub) and just dump the links into the body for now so you can click through them.

Step 1: Create the Generator Script

Create scripts/d3js/generate_hubs.py.

import json
import os
from pathlib import Path
import shutil

# --- CONFIGURATION ---
# Source Data (The Blueprint)
NAVGRAPH_FILE = Path("navgraph.json")

# Target Sandbox (The Construction Site)
# We use _hubs to keep it organized, but Jekyll will treat them as pages
TARGET_REPO = Path("/home/mike/repos/trimnoir")
HUBS_DIR = TARGET_REPO / "_hubs"

def clean_and_prep_dirs():
    """Ensures the target directory exists and is empty."""
    if HUBS_DIR.exists():
        shutil.rmtree(HUBS_DIR)
    HUBS_DIR.mkdir(parents=True, exist_ok=True)
    print(f"🧹 Cleaned and prepped: {HUBS_DIR}")

def generate_hub_file(node):
    """
    Creates a markdown file for a single hub node.
    Recurses to create children.
    """
    # 1. Determine Filename (Flat structure on disk)
    # e.g., hub_python.md or hub_root.md
    safe_id = node['id']
    filename = f"{safe_id}.md"
    filepath = HUBS_DIR / filename
    
    # 2. Build Frontmatter
    # We use the permalink from the JSON to define the URL structure
    frontmatter = f"""---
layout: page
title: "{node['title']}"
permalink: {node['permalink']}
---
"""

    # 3. Build Body Content (The Drill-Down)
    # Phase 1: Only links to Sub-Hubs
    body = f"# {node['title']}\n\n"
    
    if node.get('children_hubs'):
        body += "## Explore Topics\n"
        for child in node['children_hubs']:
            # Create a simple markdown link: [Title](Permalink)
            body += f"* [{child['title']}]({child['permalink']})\n"
    else:
        body += "*No sub-topics found.*\n"

    # (Placeholder for Articles - Phase 2)
    # body += "\n## Articles\n..."

    # 4. Write File
    with open(filepath, 'w', encoding='utf-8') as f:
        f.write(frontmatter + body)
        
    print(f"✅ Created: {filename} -> {node['permalink']}")

    # 5. Recurse (Depth-First Creation)
    for child in node.get('children_hubs', []):
        generate_hub_file(child)

def main():
    print("🚀 Starting Hub Generation...")
    
    if not NAVGRAPH_FILE.exists():
        print(f"❌ Error: {NAVGRAPH_FILE} not found. Run build_navgraph.py first.")
        return

    # Load the blueprint
    with open(NAVGRAPH_FILE, 'r', encoding='utf-8') as f:
        nav_tree = json.load(f)

    # Prepare the site
    clean_and_prep_dirs()

    # Start the recursive build from the root
    # Note: 'nav_tree' is the root node itself in our JSON structure
    generate_hub_file(nav_tree)

    print(f"\n🎉 Generation Complete.")
    print(f"📂 Check {HUBS_DIR} for your new hub pages.")
    print("👉 Next Step: Run 'jes' (or 'jekyll serve') in the trimnoir repo.")

if __name__ == "__main__":
    main()

The “Small Win” Protocol

Copy the code block above.
Save it as scripts/d3js/generate_hubs.py (using xv or your preferred method).
Git Commit: Add it to your repo so we have the history.
Run: python scripts/d3js/generate_hubs.py

This will populate /home/mike/repos/trimnoir/_hubs/ with a flat list of markdown files (hub_root.md, hub_python.md, etc.). Because of the permalink frontmatter, when you run Jekyll, they will magically appear at /, /python/, etc.

Go ahead and fire the generator. Let’s see the skeleton.

Me: Alright, we do it:

(nix) 
[mike@nixos:~/repos/pipulate/scripts/d3js]$ xv generate_hubs.py
(nix) 
[mike@nixos:~/repos/pipulate/scripts/d3js]$ python generate_hubs.py 
🚀 Starting Hub Generation...
🧹 Cleaned and prepped: /home/mike/repos/trimnoir/_hubs
✅ Created: root.md -> /
✅ Created: hub_htmx.md -> /htmx/
✅ Created: hub_llm.md -> /llm/
✅ Created: hub_llm-2.md -> /llm-2/
✅ Created: hub_htmx-2.md -> /htmx-2/
✅ Created: hub_htmx-3.md -> /htmx-3/
✅ Created: hub_fasthtml.md -> /fasthtml/
✅ Created: hub_websockets.md -> /websockets/
✅ Created: hub_ollama.md -> /ollama/
✅ Created: hub_fasthtml-2.md -> /fasthtml-2/
✅ Created: hub_fasthtml-3.md -> /fasthtml-3/
✅ Created: hub_fasthtml-4.md -> /fasthtml-4/
✅ Created: hub_htmx-4.md -> /htmx-4/
✅ Created: hub_htmx-5.md -> /htmx-5/
✅ Created: hub_python.md -> /python/
✅ Created: hub_fasthtml-5.md -> /fasthtml-5/
✅ Created: hub_fasthtml-6.md -> /fasthtml-6/
✅ Created: hub_htmx-6.md -> /htmx-6/
✅ Created: hub_htmx-7.md -> /htmx-7/
✅ Created: hub_htmx-8.md -> /htmx-8/
✅ Created: hub_python-2.md -> /python-2/
✅ Created: hub_htmx-9.md -> /htmx-9/
✅ Created: hub_htmx-10.md -> /htmx-10/
✅ Created: hub_htmx-11.md -> /htmx-11/
✅ Created: hub_htmx-12.md -> /htmx-12/
✅ Created: hub_htmx-13.md -> /htmx-13/
✅ Created: hub_htmx-14.md -> /htmx-14/
✅ Created: hub_python-3.md -> /python-3/
✅ Created: hub_llm-3.md -> /llm-3/
✅ Created: hub_antitrust.md -> /antitrust/
✅ Created: hub_websockets-2.md -> /websockets-2/
✅ Created: hub_llms.md -> /llms/
✅ Created: hub_llm-4.md -> /llm-4/
✅ Created: hub_llm-5.md -> /llm-5/
✅ Created: hub_ollama-2.md -> /ollama-2/
✅ Created: hub_pandas.md -> /pandas/
✅ Created: hub_structured-data.md -> /structured-data/
✅ Created: hub_pandas-2.md -> /pandas-2/
✅ Created: hub_pandas-3.md -> /pandas-3/
✅ Created: hub_pipulate.md -> /pipulate/
✅ Created: hub_python-4.md -> /python-4/
✅ Created: hub_pandas-4.md -> /pandas-4/
✅ Created: hub_python-5.md -> /python-5/
✅ Created: hub_htmx-15.md -> /htmx-15/
✅ Created: hub_unix-philosophy.md -> /unix-philosophy/
✅ Created: hub_flow-state.md -> /flow-state/
✅ Created: hub_llm-6.md -> /llm-6/
✅ Created: hub_selenium.md -> /selenium/
✅ Created: hub_foss.md -> /foss/
✅ Created: hub_cross-platform-development.md -> /cross-platform-development/
✅ Created: hub_atp.md -> /atp/
✅ Created: hub_innovation.md -> /innovation/
✅ Created: hub_fasthtml-7.md -> /fasthtml-7/
✅ Created: hub_fasthtml-8.md -> /fasthtml-8/
✅ Created: hub_ripgrep.md -> /ripgrep/
✅ Created: hub_management-engine-me.md -> /management-engine-me/
✅ Created: hub_git.md -> /git/
✅ Created: hub_gbekli-tepe.md -> /gbekli-tepe/
✅ Created: hub_llm-7.md -> /llm-7/
✅ Created: hub_antifragile-intelligence.md -> /antifragile-intelligence/
✅ Created: hub_meta-cognition.md -> /meta-cognition/
✅ Created: hub_ai-assisted-development.md -> /ai-assisted-development/
✅ Created: hub_ai-assisted-development-2.md -> /ai-assisted-development-2/
✅ Created: hub_negentropy.md -> /negentropy/
✅ Created: hub_dependency-management.md -> /dependency-management/
✅ Created: hub_sovereign-ai.md -> /sovereign-ai/
✅ Created: hub_jupyter-notebook.md -> /jupyter-notebook/
✅ Created: hub_htmx-16.md -> /htmx-16/
✅ Created: hub_neovim.md -> /neovim/
✅ Created: hub_refactoring.md -> /refactoring/
✅ Created: hub_git-2.md -> /git-2/
✅ Created: hub_python-6.md -> /python-6/
✅ Created: hub_web-scraping.md -> /web-scraping/
✅ Created: hub_dom-visualizer.md -> /dom-visualizer/
✅ Created: hub_ai-agents.md -> /ai-agents/
✅ Created: hub_selenium-2.md -> /selenium-2/
✅ Created: hub_urlinspector.md -> /urlinspector/
✅ Created: hub_ai-training-data.md -> /ai-training-data/
✅ Created: hub_urlinspector-2.md -> /urlinspector-2/
✅ Created: hub_ai.md -> /ai/
✅ Created: hub_python-7.md -> /python-7/
✅ Created: hub_jekyll.md -> /jekyll/
✅ Created: hub_botify.md -> /botify/
✅ Created: hub_jekyll-2.md -> /jekyll-2/
✅ Created: hub_grok-3.md -> /grok-3/
✅ Created: hub_nix-flakes.md -> /nix-flakes/
✅ Created: hub_jekyll-3.md -> /jekyll-3/
✅ Created: hub_nixos.md -> /nixos/
✅ Created: hub_keyword-clustering.md -> /keyword-clustering/
✅ Created: hub_seo.md -> /seo/
✅ Created: hub_seo-2.md -> /seo-2/
✅ Created: hub_python-8.md -> /python-8/
✅ Created: hub_ollama-3.md -> /ollama-3/
✅ Created: hub_jekyll-4.md -> /jekyll-4/
✅ Created: hub_flow-state-2.md -> /flow-state-2/
✅ Created: hub_prompt-engineering.md -> /prompt-engineering/
✅ Created: hub_prompt-engineering-2.md -> /prompt-engineering-2/
✅ Created: hub_prompt-engineering-3.md -> /prompt-engineering-3/
✅ Created: hub_prompt-engineering-4.md -> /prompt-engineering-4/
✅ Created: hub_ai-agents-2.md -> /ai-agents-2/
✅ Created: hub_prompt-engineering-5.md -> /prompt-engineering-5/
✅ Created: hub_prompt-engineering-6.md -> /prompt-engineering-6/
✅ Created: hub_prompt-engineering-7.md -> /prompt-engineering-7/
✅ Created: hub_llm-8.md -> /llm-8/
✅ Created: hub_prompt-engineering-8.md -> /prompt-engineering-8/
✅ Created: hub_git-diff.md -> /git-diff/
✅ Created: hub_htmx-17.md -> /htmx-17/
✅ Created: hub_ai-code-generation.md -> /ai-code-generation/
✅ Created: hub_llm-9.md -> /llm-9/
✅ Created: hub_htmx-18.md -> /htmx-18/
✅ Created: hub_git-3.md -> /git-3/
✅ Created: hub_debugging.md -> /debugging/
✅ Created: hub_jekyll-5.md -> /jekyll-5/
✅ Created: hub_automation.md -> /automation/
✅ Created: hub_ai-coding-assistant.md -> /ai-coding-assistant/
✅ Created: hub_ai-debugging.md -> /ai-debugging/
✅ Created: hub_human-ai-collaboration.md -> /human-ai-collaboration/
✅ Created: hub_browser-automation.md -> /browser-automation/
✅ Created: hub_ripgrep-2.md -> /ripgrep-2/
✅ Created: hub_refactoring-2.md -> /refactoring-2/
✅ Created: hub_fasthtml-9.md -> /fasthtml-9/
✅ Created: hub_workflow-automation.md -> /workflow-automation/
✅ Created: hub_code-refactoring.md -> /code-refactoring/
✅ Created: hub_ai-coding-assistant-2.md -> /ai-coding-assistant-2/
✅ Created: hub_refactoring-3.md -> /refactoring-3/
✅ Created: hub_nixos-2.md -> /nixos-2/
✅ Created: hub_selenium-refactoring.md -> /selenium-refactoring/
✅ Created: hub_gemini-cli.md -> /gemini-cli/
✅ Created: hub_ai-agents-3.md -> /ai-agents-3/
✅ Created: hub_jupyter-notebook-2.md -> /jupyter-notebook-2/
✅ Created: hub_jupyter-notebooks.md -> /jupyter-notebooks/
✅ Created: hub_jupyter-notebooks-2.md -> /jupyter-notebooks-2/
✅ Created: hub_jupyter-notebook-3.md -> /jupyter-notebook-3/
✅ Created: hub_jupyter-notebook-4.md -> /jupyter-notebook-4/
✅ Created: hub_jupyter-notebook-5.md -> /jupyter-notebook-5/
✅ Created: hub_jupyter-notebooks-3.md -> /jupyter-notebooks-3/
✅ Created: hub_jupyter-notebook-6.md -> /jupyter-notebook-6/
✅ Created: hub_jupyter-notebook-7.md -> /jupyter-notebook-7/
✅ Created: hub_jupyter-notebook-8.md -> /jupyter-notebook-8/
✅ Created: hub_jupyter-notebooks-4.md -> /jupyter-notebooks-4/
✅ Created: hub_git-4.md -> /git-4/
✅ Created: hub_jupyter-notebook-9.md -> /jupyter-notebook-9/
✅ Created: hub_jupyter-notebook-10.md -> /jupyter-notebook-10/
✅ Created: hub_nix.md -> /nix/
✅ Created: hub_nix-2.md -> /nix-2/
✅ Created: hub_vim.md -> /vim/
✅ Created: hub_nixos-3.md -> /nixos-3/
✅ Created: hub_nix-3.md -> /nix-3/
✅ Created: hub_nix-4.md -> /nix-4/
✅ Created: hub_nix-5.md -> /nix-5/
✅ Created: hub_nix-6.md -> /nix-6/
✅ Created: hub_nixos-4.md -> /nixos-4/
✅ Created: hub_nixos-5.md -> /nixos-5/
✅ Created: hub_nixos-6.md -> /nixos-6/
✅ Created: hub_nixos-7.md -> /nixos-7/
✅ Created: hub_nixos-8.md -> /nixos-8/
✅ Created: hub_nixos-9.md -> /nixos-9/
✅ Created: hub_ollama-4.md -> /ollama-4/
✅ Created: hub_nixos-10.md -> /nixos-10/
✅ Created: hub_nixos-11.md -> /nixos-11/
✅ Created: hub_nixos-12.md -> /nixos-12/
✅ Created: hub_nix-7.md -> /nix-7/
✅ Created: hub_nix-8.md -> /nix-8/
✅ Created: hub_nix-flakes-2.md -> /nix-flakes-2/
✅ Created: hub_nixos-13.md -> /nixos-13/
✅ Created: hub_nixos-14.md -> /nixos-14/
✅ Created: hub_nixos-15.md -> /nixos-15/
✅ Created: hub_nix-flakes-3.md -> /nix-flakes-3/
✅ Created: hub_nix-flakes-4.md -> /nix-flakes-4/
✅ Created: hub_selenium-3.md -> /selenium-3/
✅ Created: hub_jekyll-6.md -> /jekyll-6/
✅ Created: hub_cuda.md -> /cuda/
✅ Created: hub_nix-9.md -> /nix-9/
✅ Created: hub_ai-2.md -> /ai-2/
✅ Created: hub_nix-10.md -> /nix-10/
✅ Created: hub_radical-transparency.md -> /radical-transparency/
✅ Created: hub_llm-context.md -> /llm-context/
✅ Created: hub_ai-prompt-engineering.md -> /ai-prompt-engineering/
✅ Created: hub_nix-flakes-5.md -> /nix-flakes-5/
✅ Created: hub_ai-workflow.md -> /ai-workflow/
✅ Created: hub_radical-transparency-2.md -> /radical-transparency-2/
✅ Created: hub_ai-context.md -> /ai-context/
✅ Created: hub_ai-3.md -> /ai-3/
✅ Created: hub_ai-4.md -> /ai-4/
✅ Created: hub_future-proofing.md -> /future-proofing/
✅ Created: hub_flow-state-3.md -> /flow-state-3/
✅ Created: hub_prompt-engineering-9.md -> /prompt-engineering-9/
✅ Created: hub_information-architecture.md -> /information-architecture/
✅ Created: hub_amnesic-ai.md -> /amnesic-ai/
✅ Created: hub_htmx-19.md -> /htmx-19/
✅ Created: hub_prompt-engineering-10.md -> /prompt-engineering-10/
✅ Created: hub_iterative-development.md -> /iterative-development/
✅ Created: hub_refactoring-4.md -> /refactoring-4/
✅ Created: hub_browser-automation-2.md -> /browser-automation-2/
✅ Created: hub_sovereign-ai-2.md -> /sovereign-ai-2/
✅ Created: hub_ai-5.md -> /ai-5/
✅ Created: hub_tool-calling.md -> /tool-calling/
✅ Created: hub_nix-11.md -> /nix-11/
✅ Created: hub_ai-safety.md -> /ai-safety/
✅ Created: hub_cambrian-explosion-of-ai.md -> /cambrian-explosion-of-ai/
✅ Created: hub_llms-2.md -> /llms-2/
✅ Created: hub_information-architecture-2.md -> /information-architecture-2/
✅ Created: hub_radical-transparency-3.md -> /radical-transparency-3/
✅ Created: hub_ai-safety-2.md -> /ai-safety-2/
✅ Created: hub_nixos-16.md -> /nixos-16/
✅ Created: hub_llm-inference.md -> /llm-inference/
✅ Created: hub_cursor-ai.md -> /cursor-ai/
✅ Created: hub_seo-3.md -> /seo-3/
✅ Created: hub_cursor-ai-2.md -> /cursor-ai-2/
✅ Created: hub_local-llm.md -> /local-llm/
✅ Created: hub_neovim-2.md -> /neovim-2/
✅ Created: hub_ai-6.md -> /ai-6/
✅ Created: hub_ikigai.md -> /ikigai/
✅ Created: hub_llm-10.md -> /llm-10/
✅ Created: hub_rag.md -> /rag/
✅ Created: hub_workflow-automation-2.md -> /workflow-automation-2/
✅ Created: hub_nixos-17.md -> /nixos-17/
✅ Created: hub_nix-12.md -> /nix-12/
✅ Created: hub_namedtuple.md -> /namedtuple/
✅ Created: hub_sovereign-ai-3.md -> /sovereign-ai-3/
✅ Created: hub_workflow-automation-3.md -> /workflow-automation-3/
✅ Created: hub_ai-persistence.md -> /ai-persistence/

🎉 Generation Complete.
📂 Check /home/mike/repos/trimnoir/_hubs for your new hub pages.
👉 Next Step: Run 'jes' (or 'jekyll serve') in the trimnoir repo.
(nix) 
[mike@nixos:~/repos/pipulate/scripts/d3js]$ 

Me: Okay, generating those files I believe worked perfectly:

[mike@nixos:~/repos/trimnoir]$ ls
404.html  about.markdown  _config.yml  flake.lock  flake.nix  Gemfile  Gemfile.lock  _hubs  index.markdown  _posts  _site

[mike@nixos:~/repos/trimnoir]$ cd _hubs/

[mike@nixos:~/repos/trimnoir/_hubs]$ ls
hub_ai-2.md                        hub_git-3.md                       hub_llm-6.md                 hub_pandas-4.md
hub_ai-3.md                        hub_git-4.md                       hub_llm-7.md                 hub_pandas.md
hub_ai-4.md                        hub_git-diff.md                    hub_llm-8.md                 hub_pipulate.md
hub_ai-5.md                        hub_git.md                         hub_llm-9.md                 hub_prompt-engineering-10.md
hub_ai-6.md                        hub_grok-3.md                      hub_llm-context.md           hub_prompt-engineering-2.md
hub_ai-agents-2.md                 hub_htmx-10.md                     hub_llm-inference.md         hub_prompt-engineering-3.md
hub_ai-agents-3.md                 hub_htmx-11.md                     hub_llm.md                   hub_prompt-engineering-4.md
hub_ai-agents.md                   hub_htmx-12.md                     hub_llms-2.md                hub_prompt-engineering-5.md
hub_ai-assisted-development-2.md   hub_htmx-13.md                     hub_llms.md                  hub_prompt-engineering-6.md
hub_ai-assisted-development.md     hub_htmx-14.md                     hub_local-llm.md             hub_prompt-engineering-7.md
hub_ai-code-generation.md          hub_htmx-15.md                     hub_management-engine-me.md  hub_prompt-engineering-8.md
hub_ai-coding-assistant-2.md       hub_htmx-16.md                     hub_meta-cognition.md        hub_prompt-engineering-9.md
hub_ai-coding-assistant.md         hub_htmx-17.md                     hub_namedtuple.md            hub_prompt-engineering.md
hub_ai-context.md                  hub_htmx-18.md                     hub_negentropy.md            hub_python-2.md
hub_ai-debugging.md                hub_htmx-19.md                     hub_neovim-2.md              hub_python-3.md
hub_ai.md                          hub_htmx-2.md                      hub_neovim.md                hub_python-4.md
hub_ai-persistence.md              hub_htmx-3.md                      hub_nix-10.md                hub_python-5.md
hub_ai-prompt-engineering.md       hub_htmx-4.md                      hub_nix-11.md                hub_python-6.md
hub_ai-safety-2.md                 hub_htmx-5.md                      hub_nix-12.md                hub_python-7.md
hub_ai-safety.md                   hub_htmx-6.md                      hub_nix-2.md                 hub_python-8.md
hub_ai-training-data.md            hub_htmx-7.md                      hub_nix-3.md                 hub_python.md
hub_ai-workflow.md                 hub_htmx-8.md                      hub_nix-4.md                 hub_radical-transparency-2.md
hub_amnesic-ai.md                  hub_htmx-9.md                      hub_nix-5.md                 hub_radical-transparency-3.md
hub_antifragile-intelligence.md    hub_htmx.md                        hub_nix-6.md                 hub_radical-transparency.md
hub_antitrust.md                   hub_human-ai-collaboration.md      hub_nix-7.md                 hub_rag.md
hub_atp.md                         hub_ikigai.md                      hub_nix-8.md                 hub_refactoring-2.md
hub_automation.md                  hub_information-architecture-2.md  hub_nix-9.md                 hub_refactoring-3.md
hub_botify.md                      hub_information-architecture.md    hub_nix-flakes-2.md          hub_refactoring-4.md
hub_browser-automation-2.md        hub_innovation.md                  hub_nix-flakes-3.md          hub_refactoring.md
hub_browser-automation.md          hub_iterative-development.md       hub_nix-flakes-4.md          hub_ripgrep-2.md
hub_cambrian-explosion-of-ai.md    hub_jekyll-2.md                    hub_nix-flakes-5.md          hub_ripgrep.md
hub_code-refactoring.md            hub_jekyll-3.md                    hub_nix-flakes.md            hub_selenium-2.md
hub_cross-platform-development.md  hub_jekyll-4.md                    hub_nix.md                   hub_selenium-3.md
hub_cuda.md                        hub_jekyll-5.md                    hub_nixos-10.md              hub_selenium.md
hub_cursor-ai-2.md                 hub_jekyll-6.md                    hub_nixos-11.md              hub_selenium-refactoring.md
hub_cursor-ai.md                   hub_jekyll.md                      hub_nixos-12.md              hub_seo-2.md
hub_debugging.md                   hub_jupyter-notebook-10.md         hub_nixos-13.md              hub_seo-3.md
hub_dependency-management.md       hub_jupyter-notebook-2.md          hub_nixos-14.md              hub_seo.md
hub_dom-visualizer.md              hub_jupyter-notebook-3.md          hub_nixos-15.md              hub_sovereign-ai-2.md
hub_fasthtml-2.md                  hub_jupyter-notebook-4.md          hub_nixos-16.md              hub_sovereign-ai-3.md
hub_fasthtml-3.md                  hub_jupyter-notebook-5.md          hub_nixos-17.md              hub_sovereign-ai.md
hub_fasthtml-4.md                  hub_jupyter-notebook-6.md          hub_nixos-2.md               hub_structured-data.md
hub_fasthtml-5.md                  hub_jupyter-notebook-7.md          hub_nixos-3.md               hub_tool-calling.md
hub_fasthtml-6.md                  hub_jupyter-notebook-8.md          hub_nixos-4.md               hub_unix-philosophy.md
hub_fasthtml-7.md                  hub_jupyter-notebook-9.md          hub_nixos-5.md               hub_urlinspector-2.md
hub_fasthtml-8.md                  hub_jupyter-notebook.md            hub_nixos-6.md               hub_urlinspector.md
hub_fasthtml-9.md                  hub_jupyter-notebooks-2.md         hub_nixos-7.md               hub_vim.md
hub_fasthtml.md                    hub_jupyter-notebooks-3.md         hub_nixos-8.md               hub_web-scraping.md
hub_flow-state-2.md                hub_jupyter-notebooks-4.md         hub_nixos-9.md               hub_websockets-2.md
hub_flow-state-3.md                hub_jupyter-notebooks.md           hub_nixos.md                 hub_websockets.md
hub_flow-state.md                  hub_keyword-clustering.md          hub_ollama-2.md              hub_workflow-automation-2.md
hub_foss.md                        hub_llm-10.md                      hub_ollama-3.md              hub_workflow-automation-3.md
hub_future-proofing.md             hub_llm-2.md                       hub_ollama-4.md              hub_workflow-automation.md
hub_gbekli-tepe.md                 hub_llm-3.md                       hub_ollama.md                root.md
hub_gemini-cli.md                  hub_llm-4.md                       hub_pandas-2.md
hub_git-2.md                       hub_llm-5.md                       hub_pandas-3.md

[mike@nixos:~/repos/trimnoir/_hubs]$ cd ..

[mike@nixos:~/repos/trimnoir]$ lsp
/home/mike/repos/trimnoir/404.html
/home/mike/repos/trimnoir/about.markdown
/home/mike/repos/trimnoir/_config.yml
/home/mike/repos/trimnoir/flake.lock
/home/mike/repos/trimnoir/flake.nix
/home/mike/repos/trimnoir/Gemfile
/home/mike/repos/trimnoir/Gemfile.lock
/home/mike/repos/trimnoir/_hubs
/home/mike/repos/trimnoir/index.markdown
/home/mike/repos/trimnoir/_posts
/home/mike/repos/trimnoir/_site

[mike@nixos:~/repos/trimnoir]$ 

And so we bank it:

(nix) 
[mike@nixos:~/repos/pipulate/scripts/d3js]$ git commit -am "Adding version 1 of generating hub pages for Jekyll"
[main 9cdaa8d4] Adding version 1 of generating hub pages for Jekyll
 3 files changed, 100 insertions(+), 17 deletions(-)
 create mode 100644 scripts/d3js/generate_hubs.py
(nix) 
[mike@nixos:~/repos/pipulate/scripts/d3js]$ git push
Enumerating objects: 12, done.
Counting objects: 100% (12/12), done.
Delta compression using up to 48 threads
Compressing objects: 100% (7/7), done.
Writing objects: 100% (7/7), 2.05 KiB | 2.05 MiB/s, done.
Total 7 (delta 5), reused 0 (delta 0), pack-reused 0 (from 0)
remote: Resolving deltas: 100% (5/5), completed with 5 local objects.
To github.com:miklevin/pipulate
   cfe8cb4e..9cdaa8d4  main -> main
(nix) 
[mike@nixos:~/repos/pipulate/scripts/d3js]$

But now a couple of things. I think those folders prefixed with an underscore actually don’t get generated. I tried visiting:

http://localhost:4003/cuda/

…and it’s the 404 page. Also even though there’s a homepage there index.markdown we can totally overwrite that with a point of entry. I can delete that manually and we should use whatever (or maybe it’s already done) we use as our homepage in hub generation.

Addressing Jekyll’s Underscore Quandary

Refining Generation: Visible Hubs and Homepage Takeover

Gemini: You nailed the diagnosis. In Jekyll, folders starting with an underscore (like _hubs, _layouts, _includes) are treated as special “hidden” directories by default. Jekyll won’t look inside them for pages to render unless you explicitly configure them as a “Collection.”

To keep this “Low Tech Liability” and avoid touching _config.yml for now, the path of least resistance is to simply rename the target folder to pages (no underscore) or just put them in the root.

But we can do better. We can modify the script to:

**Output Hubs to pages/**: A standard, visible folder that keeps your root clean.
Hijack the Homepage: Detect the “Root” node and write it directly to index.md in the main repository root, overwriting the default Jekyll intro.

Here is the v2 generate_hubs.py. It fixes the visibility issue and claims the homepage throne.

The Fix: `scripts/d3js/generate_hubs.py`

import json
import os
from pathlib import Path
import shutil

# --- CONFIGURATION ---
NAVGRAPH_FILE = Path("navgraph.json")
TARGET_REPO = Path("/home/mike/repos/trimnoir")

# 1. Change _hubs to pages so Jekyll sees them automatically
HUBS_DIR = TARGET_REPO / "pages" 

def clean_and_prep_dirs():
    """Ensures the target directory exists and is empty."""
    if HUBS_DIR.exists():
        shutil.rmtree(HUBS_DIR)
    HUBS_DIR.mkdir(parents=True, exist_ok=True)
    print(f"🧹 Cleaned and prepped: {HUBS_DIR}")

def generate_hub_file(node):
    """
    Creates a markdown file for a single hub node.
    Recurses to create children.
    """
    safe_id = node['id']
    
    # --- SPECIAL HANDLING FOR ROOT ---
    # If this is the root node, we overwrite the main index.md
    if node.get('id') == 'root' or node.get('permalink') == '/':
        filename = "index.md"
        filepath = TARGET_REPO / filename
        print(f"🏠 Overwriting Homepage: {filepath}")
    else:
        # Standard Hubs go into /pages/
        filename = f"{safe_id}.md"
        filepath = HUBS_DIR / filename
    
    # 2. Build Frontmatter
    frontmatter = f"""---
layout: page
title: "{node['title']}"
permalink: {node['permalink']}
---
"""

    # 3. Build Body (The Drill-Down)
    body = f"# {node['title']}\n\n"
    
    # Add Description/Blurb if available (from your articles)
    if node.get('blurb'):
        body += f"_{node['blurb']}_\n\n"
    
    # Render Sub-Hubs
    if node.get('children_hubs'):
        body += "## Explore Topics\n"
        for child in node['children_hubs']:
            body += f"* [{child['title']}]({child['permalink']})\n"
    
    # Render Articles (The "Gold Pan" items)
    if node.get('children_articles'):
        body += "\n## Top Articles\n"
        for article in node['children_articles']:
            # Use the article's own permalink
            body += f"* [{article['title']}]({article['permalink']})\n"
            if 'date' in article:
                body += f"  <small>{article['date']}</small>\n"

    if not node.get('children_hubs') and not node.get('children_articles'):
        body += "*No sub-topics found.*\n"

    # 4. Write File
    with open(filepath, 'w', encoding='utf-8') as f:
        f.write(frontmatter + body)
        
    # 5. Recurse
    for child in node.get('children_hubs', []):
        generate_hub_file(child)

def main():
    print("🚀 Starting Hub Generation v2...")
    
    if not NAVGRAPH_FILE.exists():
        print(f"❌ Error: {NAVGRAPH_FILE} not found.")
        return

    with open(NAVGRAPH_FILE, 'r', encoding='utf-8') as f:
        nav_tree = json.load(f)

    # Clean the pages directory
    clean_and_prep_dirs()
    
    # Nuke the old default index if it exists (Jekyll defaults to index.markdown sometimes)
    old_index = TARGET_REPO / "index.markdown"
    if old_index.exists():
        os.remove(old_index)
        print("🗑️  Removed default index.markdown")

    generate_hub_file(nav_tree)

    print(f"\n🎉 Generation Complete.")
    print(f"📂 Hubs are in {HUBS_DIR}")
    print(f"🏠 Homepage is at {TARGET_REPO}/index.md")

if __name__ == "__main__":
    main()

Explanation of Changes

Directory Change: Switched from _hubs to pages. Jekyll renders folders without underscores by default. This makes them “live” immediately.
Root Hijack: The script now checks if a node is root. If so, it writes directly to trimnoir/index.md, effectively taking over the homepage.
Cleanup: It actively deletes the default index.markdown if it finds one, preventing conflicts (Jekyll gets confused if you have both index.md and index.markdown).
Article Rendering: I enabled the “Phase 2” placeholder. It now actually lists the “Gold Pan” articles (the top 5-9) on the hub pages, so you can see the content mix immediately.

Update the file, run it, and then check localhost:4000. You should see your new AI-generated homepage.

Me: Okay, here’s the diff:

(nix) 
[mike@nixos:~/repos/pipulate/scripts/d3js]$ git --no-pager diff -- generate_hubs.py
diff --git a/scripts/d3js/generate_hubs.py b/scripts/d3js/generate_hubs.py
index 84a2a021..791b03d2 100644
--- a/scripts/d3js/generate_hubs.py
+++ b/scripts/d3js/generate_hubs.py
@@ -4,13 +4,11 @@ from pathlib import Path
 import shutil
 
 # --- CONFIGURATION ---
-# Source Data (The Blueprint)
 NAVGRAPH_FILE = Path("navgraph.json")
-
-# Target Sandbox (The Construction Site)
-# We use _hubs to keep it organized, but Jekyll will treat them as pages
 TARGET_REPO = Path("/home/mike/repos/trimnoir")
-HUBS_DIR = TARGET_REPO / "_hubs"
+
+# 1. Change _hubs to pages so Jekyll sees them automatically
+HUBS_DIR = TARGET_REPO / "pages" 
 
 def clean_and_prep_dirs():
     """Ensures the target directory exists and is empty."""
@@ -24,14 +22,20 @@ def generate_hub_file(node):
     Creates a markdown file for a single hub node.
     Recurses to create children.
     """
-    # 1. Determine Filename (Flat structure on disk)
-    # e.g., hub_python.md or hub_root.md
     safe_id = node['id']
-    filename = f"{safe_id}.md"
-    filepath = HUBS_DIR / filename
+    
+    # --- SPECIAL HANDLING FOR ROOT ---
+    # If this is the root node, we overwrite the main index.md
+    if node.get('id') == 'root' or node.get('permalink') == '/':
+        filename = "index.md"
+        filepath = TARGET_REPO / filename
+        print(f"🏠 Overwriting Homepage: {filepath}")
+    else:
+        # Standard Hubs go into /pages/
+        filename = f"{safe_id}.md"
+        filepath = HUBS_DIR / filename
     
     # 2. Build Frontmatter
-    # We use the permalink from the JSON to define the URL structure
     frontmatter = f"""---
 layout: page
 title: "{node['title']}"
@@ -39,52 +43,63 @@ permalink: {node['permalink']}
 ---
 """
 
-    # 3. Build Body Content (The Drill-Down)
-    # Phase 1: Only links to Sub-Hubs
+    # 3. Build Body (The Drill-Down)
     body = f"# {node['title']}\n\n"
     
+    # Add Description/Blurb if available (from your articles)
+    if node.get('blurb'):
+        body += f"_{node['blurb']}_\n\n"
+    
+    # Render Sub-Hubs
     if node.get('children_hubs'):
         body += "## Explore Topics\n"
         for child in node['children_hubs']:
-            # Create a simple markdown link: [Title](Permalink)
             body += f"* [{child['title']}]({child['permalink']})\n"
-    else:
-        body += "*No sub-topics found.*\n"
+    
+    # Render Articles (The "Gold Pan" items)
+    if node.get('children_articles'):
+        body += "\n## Top Articles\n"
+        for article in node['children_articles']:
+            # Use the article's own permalink
+            body += f"* [{article['title']}]({article['permalink']})\n"
+            if 'date' in article:
+                body += f"  <small>{article['date']}</small>\n"
 
-    # (Placeholder for Articles - Phase 2)
-    # body += "\n## Articles\n..."
+    if not node.get('children_hubs') and not node.get('children_articles'):
+        body += "*No sub-topics found.*\n"
 
     # 4. Write File
     with open(filepath, 'w', encoding='utf-8') as f:
         f.write(frontmatter + body)
         
-    print(f"✅ Created: {filename} -> {node['permalink']}")
-
-    # 5. Recurse (Depth-First Creation)
+    # 5. Recurse
     for child in node.get('children_hubs', []):
         generate_hub_file(child)
 
 def main():
-    print("🚀 Starting Hub Generation...")
+    print("🚀 Starting Hub Generation v2...")
     
     if not NAVGRAPH_FILE.exists():
-        print(f"❌ Error: {NAVGRAPH_FILE} not found. Run build_navgraph.py first.")
+        print(f"❌ Error: {NAVGRAPH_FILE} not found.")
         return
 
-    # Load the blueprint
     with open(NAVGRAPH_FILE, 'r', encoding='utf-8') as f:
         nav_tree = json.load(f)
 
-    # Prepare the site
+    # Clean the pages directory
     clean_and_prep_dirs()
+    
+    # Nuke the old default index if it exists (Jekyll defaults to index.markdown sometimes)
+    old_index = TARGET_REPO / "index.markdown"
+    if old_index.exists():
+        os.remove(old_index)
+        print("🗑️  Removed default index.markdown")
 
-    # Start the recursive build from the root
-    # Note: 'nav_tree' is the root node itself in our JSON structure
     generate_hub_file(nav_tree)
 
     print(f"\n🎉 Generation Complete.")
-    print(f"📂 Check {HUBS_DIR} for your new hub pages.")
-    print("👉 Next Step: Run 'jes' (or 'jekyll serve') in the trimnoir repo.")
+    print(f"📂 Hubs are in {HUBS_DIR}")
+    print(f"🏠 Homepage is at {TARGET_REPO}/index.md")
 
 if __name__ == "__main__":
     main()
\ No newline at end of file
(nix) 
[mike@nixos:~/repos/pipulate/scripts/d3js]$

Orchestrating the Hybrid Homepage

Wow, that’s a lot more diff than I thought it would be, but it worked. I also manually deleted index.markdown so there’s no ambiguity. The homepage the system generates works. But there’s some sort of cross-cutting site navigation that you layered in that is neither right, nor should it be there at all. Like the whole point of this site is that crawling it will create the link-graph we discussed and cross-cutting navigation especially of that sort that short-circuits down to the lower levels fubars that.

This first implementation should be 1-way drill-down navigation where only deep-dives are possible following the lineage links. We will use the back button to “go back up” to the homepage. We need to get the mental model that’s projected from the site surfing experience to exactly match what the link graph we’ve been discussing suggests. This is one of those cases where the world of terrible nav links that you’ve been trained on is throwing off this purity test. Once we have the ideal for drawing that link-graph we will make adjustments for the AI and human visitors to the site. Let’s strip it down and clean it up. Also it’s worth noting I have no idea where the local Minima template stuff is put or if it’s even copied local. We’re going to need to do something to get files into a _layouts/ folder too so we can start overriding it I presume.

Implementing a Minimalist, Drill-Down Layout

Gemini:

The Purge: Removing the Cross-Cutting Contamination

You are absolutely right. The standard Jekyll minima theme has a “header” navigation that automatically slurps up every page it finds and plasters it at the top of the site. This creates “wormholes” that bypass our carefully constructed “Rule of 7” hierarchy. It turns our beautiful tree into a tangled mess of edges.

We need to perform a “Header-ectomy.”

Since we don’t know where the theme files are hidden (they are buried deep in the Nix store inside the gem path), we will override the default layout by creating our own local _layouts/page.html (or default.html).

This is the “Low Tech Liability” way to fix themes: don’t edit the gem, just shadow the file.

Step 1: Create the “Clean” Layout

We need a minimalist layout that does only what we tell it to: render the content. No automatic menus. No helpful headers. Just the drill-down links we generated.

Let’s create _layouts/default.html in your trimnoir repo. This will override the theme’s default.

The Action Plan:

Create _layouts directory in trimnoir.
Create _layouts/default.html with a stripped-down HTML skeleton.
Update generate_hubs.py to use this layout (or rely on Jekyll falling back to default).

The Files

**File 1: /home/mike/repos/trimnoir/_layouts/default.html** (This is a bare-bones template. No header navigation. Just a “Home” link for safety.)

<!DOCTYPE html>
<html lang="{{ page.lang | default: site.lang | default: "en" }}">
  <head>
    <meta charset="utf-8">
    <meta http-equiv="X-UA-Compatible" content="IE=edge">
    <meta name="viewport" content="width=device-width, initial-scale=1">
    <title>{% if page.title %}{{ page.title | escape }}{% else %}{{ site.title | escape }}{% endif %}</title>
    <meta name="description" content="{{ page.description | default: site.description | strip_html | normalize_whitespace | truncate: 160 | escape }}">
    <link rel="stylesheet" href="{{ "/assets/main.css" | relative_url }}">
  </head>
  <body>
    <main class="page-content" aria-label="Content">
      <div class="wrapper">
        {% unless page.url == "/" %}
        <nav class="site-nav">
            <a href="/">Home</a> 
            </nav>
        {% endunless %}

        {{ content }}
      </div>
    </main>
  </body>
</html>

**File 2: /home/mike/repos/trimnoir/_layouts/page.html** (Just inherits from default so we don’t have to think about it).

---
layout: default
---
<article class="post">
  <header class="post-header">
    <h1 class="post-title">{{ page.title | escape }}</h1>
  </header>
  <div class="post-content">
    {{ content }}
  </div>
</article>

Step 2: Update `generate_hubs.py` (No Changes Needed to Logic)

The script already sets layout: page in the frontmatter. By creating the local _layouts/page.html and _layouts/default.html, Jekyll will automatically use our clean versions instead of the minima theme’s versions.

Execution

Create the directory: mkdir -p /home/mike/repos/trimnoir/_layouts
Create the files: Use xv or vim to create the two HTML files above.
Re-build: Run jes (or jekyll build) in trimnoir to regenerate the site with the new layouts.

This will strip out the “Helpful” auto-navigation bar and leave you with the pure, unadulterated drill-down experience. The only way down is through the links we built. The only way up is the “Home” link or the browser back button.

Shall I write a script to generate these layout files for you, or do you want to hand-craft them?

Me: Okay, so we do that. We’ll hand craft them later. But neither do I need you to create a script for me to make them. A vimmer with xclip aliases can do text jokeying easily enough, LOL. But I did have to move some files I accidentally created in the wrong place. But it’s now working exactly as intended!

[mike@nixos:~/repos/trimnoir]$ mkdir _layouts

[mike@nixos:~/repos/trimnoir]$ xv default.html

[mike@nixos:~/repos/trimnoir]$ xv page.html

[mike@nixos:~/repos/trimnoir]$ mv default.html _layouts/

[mike@nixos:~/repos/trimnoir]$ mv page.html _layouts/

[mike@nixos:~/repos/trimnoir]$ git add _layouts/*

[mike@nixos:~/repos/trimnoir]$ git status
On branch main
Your branch is up to date with 'local_origin/main'.

Changes to be committed:
  (use "git restore --staged <file>..." to unstage)
	new file:   _layouts/default.html
	new file:   _layouts/page.html
	deleted:    index.markdown

Untracked files:
  (use "git add <file>..." to include in what will be committed)
	index.md
	pages/


[mike@nixos:~/repos/trimnoir]$ vim .gitignore 

[mike@nixos:~/repos/trimnoir]$ git status
On branch main
Your branch is up to date with 'local_origin/main'.

Changes to be committed:
  (use "git restore --staged <file>..." to unstage)
	new file:   _layouts/default.html
	new file:   _layouts/page.html
	deleted:    index.markdown

Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git restore <file>..." to discard changes in working directory)
	modified:   .gitignore

Untracked files:
  (use "git add <file>..." to include in what will be committed)
	index.md


[mike@nixos:~/repos/trimnoir]$ git commit -am "Version 1 of idealized hierarchial nav working"
[main 8cba406] Version 1 of idealized hierarchial nav working
 4 files changed, 36 insertions(+), 6 deletions(-)
 create mode 100644 _layouts/default.html
 create mode 100644 _layouts/page.html
 delete mode 100644 index.markdown

[mike@nixos:~/repos/trimnoir]$ git push
Enumerating objects: 8, done.
Counting objects: 100% (8/8), done.
Delta compression using up to 48 threads
Compressing objects: 100% (6/6), done.
Writing objects: 100% (6/6), 1.01 KiB | 1.01 MiB/s, done.
Total 6 (delta 2), reused 0 (delta 0), pack-reused 0 (from 0)
To /home/mike/git-repos/trimnoir.git
   9c85562..8cba406  main -> main

[mike@nixos:~/repos/trimnoir]$

Did you make the index.md in the repo root? I think what we might end up doing is creating a sample of the top-node (homepage’s) links in a file inside an _includes/ folder so it can be used as a Jekyll (Liquid Template) include file on a hand-crafted homepage so I have the freedom of the homepage being free from the hub-page generation system. Homepages are always exceptions this way. But it will still get the benefit of the link-generation system. I’ll make that folder so you don’t have to worry about the making of it in the updated script. You can just plop the include in there and update the index.md to use it.

[mike@nixos:~/repos/trimnoir]$ mkdir _includes

[mike@nixos:~/repos/trimnoir]$

Please and thank you!

Gemini: Context verified. We are in the final stages of the “Construction Engine,” refining the Jekyll implementation of the NavGraph.

The user has successfully generated the hub pages and cleaned up the layouts manually. Now, the focus is on handling the Homepage (index.md) as a special case.

The user wants to decouple the homepage content from the automated generation logic while still benefiting from the dynamic link structure. The proposed solution is to extract the generated links for the root node into a Jekyll include file (_includes/root_links.html or similar) and then have a hand-crafted index.md that simply includes this file. This allows the homepage to have custom marketing copy or layout while keeping the navigation data automated.

I need to update scripts/d3js/generate_hubs.py to:

Detect the root node.
Instead of overwriting index.md entirely, generate the navigation links into _includes/nav_root.html (or similar).
Update (or create if missing) index.md to ensure it has the {% include nav_root.html %} tag, but otherwise leave it alone (or generate a default one if it doesn’t exist that uses the include).

Let’s refine the script to support this “Hybrid Homepage” model.

Updated Plan: The “Hybrid Homepage” Generator

We are shifting from a “Hostile Takeover” of the homepage to a “Helpful Injection.”

Instead of overwriting index.md every time, we will:

Generate the drill-down links for the root node into a partial: _includes/nav_root.html.
Create a default index.md only if it doesn’t exist, which includes that partial.

This gives you the freedom to hand-craft the homepage narrative while keeping the “Rule of 7” navigation live and automated.

The Code: `scripts/d3js/generate_hubs.py`

import json
import os
from pathlib import Path
import shutil

# --- CONFIGURATION ---
NAVGRAPH_FILE = Path("navgraph.json")
TARGET_REPO = Path("/home/mike/repos/trimnoir")

# Output Locations
HUBS_DIR = TARGET_REPO / "pages" 
INCLUDES_DIR = TARGET_REPO / "_includes"
INDEX_FILE = TARGET_REPO / "index.md"

def clean_and_prep_dirs():
    """Ensures target directories exist."""
    if HUBS_DIR.exists():
        shutil.rmtree(HUBS_DIR)
    HUBS_DIR.mkdir(parents=True, exist_ok=True)
    INCLUDES_DIR.mkdir(parents=True, exist_ok=True)
    print(f"🧹 Cleaned pages/ and checked _includes/")

def render_links_block(node):
    """Helper to generate the markdown link list for a node."""
    body = ""
    
    # Render Sub-Hubs
    if node.get('children_hubs'):
        body += "\n## Explore Topics\n"
        for child in node['children_hubs']:
            body += f"* [{child['title']}]({child['permalink']})\n"
    
    # Render Articles
    if node.get('children_articles'):
        body += "\n## Top Articles\n"
        for article in node['children_articles']:
            body += f"* [{article['title']}]({article['permalink']})\n"
            if 'date' in article:
                body += f"  <small>{article['date']}</small>\n"
                
    return body

def generate_root_include(node):
    """
    Generates _includes/nav_root.html with JUST the links.
    This allows the homepage to be hand-crafted while importing the nav.
    """
    content = render_links_block(node)
    
    # We use HTML/Markdown mix for includes usually, but let's stick to markdown 
    # since Jekyll includes parse markdown by default in many contexts, 
    # or we can wrap it in a div if needed. For now, raw markdown is safest.
    
    include_path = INCLUDES_DIR / "nav_root.md"
    with open(include_path, 'w', encoding='utf-8') as f:
        f.write(content)
    
    print(f"🏠 Generated Root Navigation Include: {include_path}")

    # Create a default index.md ONLY if it doesn't exist
    if not INDEX_FILE.exists():
        default_index = """---
layout: page
title: "Home"
permalink: /
---

# Welcome to the Knowledge Base

This is the root of the graph.

{% include nav_root.md %}
"""
        with open(INDEX_FILE, 'w', encoding='utf-8') as f:
            f.write(default_index)
        print(f"🆕 Created default Homepage: {INDEX_FILE}")
    else:
        print(f"ℹ️  Skipped overwriting existing Homepage: {INDEX_FILE}")

def generate_hub_page(node):
    """Standard Hub Page Generation (Overwrites every time)"""
    safe_id = node['id']
    filename = f"{safe_id}.md"
    filepath = HUBS_DIR / filename
    
    frontmatter = f"""---
layout: page
title: "{node['title']}"
permalink: {node['permalink']}
---
"""
    body = f"# {node['title']}\n\n"
    if node.get('blurb'):
        body += f"_{node['blurb']}_\n\n"
        
    body += render_links_block(node)

    with open(filepath, 'w', encoding='utf-8') as f:
        f.write(frontmatter + body)

def process_node(node):
    """Recursive driver."""
    # Special handling for Root
    if node.get('id') == 'root' or node.get('permalink') == '/':
        generate_root_include(node)
    else:
        generate_hub_page(node)
        
    # Recurse
    for child in node.get('children_hubs', []):
        process_node(child)

def main():
    print("🚀 Starting Hub Generation v3 (Hybrid Homepage)...")
    
    if not NAVGRAPH_FILE.exists():
        print(f"❌ Error: {NAVGRAPH_FILE} not found.")
        return

    with open(NAVGRAPH_FILE, 'r', encoding='utf-8') as f:
        nav_tree = json.load(f)

    clean_and_prep_dirs()
    
    # Nuke the old default index.markdown if it exists (Jekyll default)
    # We want to force usage of our index.md if we create it
    old_index = TARGET_REPO / "index.markdown"
    if old_index.exists():
        os.remove(old_index)
        print("🗑️  Removed default index.markdown")

    process_node(nav_tree)

    print(f"\n🎉 Generation Complete.")

if __name__ == "__main__":
    main()

Me: Okie dokey. We do the ‘ol paste-and-pin the diff:

(nix) 
[mike@nixos:~/repos/pipulate/scripts/d3js]$ xv generate_hubs.py 
(nix) 
[mike@nixos:~/repos/pipulate/scripts/d3js]$ git --no-pager diff
diff --git a/scripts/d3js/generate_hubs.py b/scripts/d3js/generate_hubs.py
index 791b03d2..c8d94577 100644
--- a/scripts/d3js/generate_hubs.py
+++ b/scripts/d3js/generate_hubs.py
@@ -7,77 +7,111 @@ import shutil
 NAVGRAPH_FILE = Path("navgraph.json")
 TARGET_REPO = Path("/home/mike/repos/trimnoir")
 
-# 1. Change _hubs to pages so Jekyll sees them automatically
+# Output Locations
 HUBS_DIR = TARGET_REPO / "pages" 
+INCLUDES_DIR = TARGET_REPO / "_includes"
+INDEX_FILE = TARGET_REPO / "index.md"
 
 def clean_and_prep_dirs():
-    """Ensures the target directory exists and is empty."""
+    """Ensures target directories exist."""
     if HUBS_DIR.exists():
         shutil.rmtree(HUBS_DIR)
     HUBS_DIR.mkdir(parents=True, exist_ok=True)
-    print(f"🧹 Cleaned and prepped: {HUBS_DIR}")
+    INCLUDES_DIR.mkdir(parents=True, exist_ok=True)
+    print(f"🧹 Cleaned pages/ and checked _includes/")
 
-def generate_hub_file(node):
+def render_links_block(node):
+    """Helper to generate the markdown link list for a node."""
+    body = ""
+    
+    # Render Sub-Hubs
+    if node.get('children_hubs'):
+        body += "\n## Explore Topics\n"
+        for child in node['children_hubs']:
+            body += f"* [{child['title']}]({child['permalink']})\n"
+    
+    # Render Articles
+    if node.get('children_articles'):
+        body += "\n## Top Articles\n"
+        for article in node['children_articles']:
+            body += f"* [{article['title']}]({article['permalink']})\n"
+            if 'date' in article:
+                body += f"  <small>{article['date']}</small>\n"
+                
+    return body
+
+def generate_root_include(node):
     """
-    Creates a markdown file for a single hub node.
-    Recurses to create children.
+    Generates _includes/nav_root.html with JUST the links.
+    This allows the homepage to be hand-crafted while importing the nav.
     """
-    safe_id = node['id']
+    content = render_links_block(node)
     
-    # --- SPECIAL HANDLING FOR ROOT ---
-    # If this is the root node, we overwrite the main index.md
-    if node.get('id') == 'root' or node.get('permalink') == '/':
-        filename = "index.md"
-        filepath = TARGET_REPO / filename
-        print(f"🏠 Overwriting Homepage: {filepath}")
+    # We use HTML/Markdown mix for includes usually, but let's stick to markdown 
+    # since Jekyll includes parse markdown by default in many contexts, 
+    # or we can wrap it in a div if needed. For now, raw markdown is safest.
+    
+    include_path = INCLUDES_DIR / "nav_root.md"
+    with open(include_path, 'w', encoding='utf-8') as f:
+        f.write(content)
+    
+    print(f"🏠 Generated Root Navigation Include: {include_path}")
+
+    # Create a default index.md ONLY if it doesn't exist
+    if not INDEX_FILE.exists():
+        default_index = """---
+layout: page
+title: "Home"
+permalink: /
+---
+
+# Welcome to the Knowledge Base
+
+This is the root of the graph.
+
+{% include nav_root.md %}
+"""
+        with open(INDEX_FILE, 'w', encoding='utf-8') as f:
+            f.write(default_index)
+        print(f"🆕 Created default Homepage: {INDEX_FILE}")
     else:
-        # Standard Hubs go into /pages/
-        filename = f"{safe_id}.md"
-        filepath = HUBS_DIR / filename
+        print(f"ℹ️  Skipped overwriting existing Homepage: {INDEX_FILE}")
+
+def generate_hub_page(node):
+    """Standard Hub Page Generation (Overwrites every time)"""
+    safe_id = node['id']
+    filename = f"{safe_id}.md"
+    filepath = HUBS_DIR / filename
     
-    # 2. Build Frontmatter
     frontmatter = f"""---
 layout: page
 title: "{node['title']}"
 permalink: {node['permalink']}
 ---
 """
-
-    # 3. Build Body (The Drill-Down)
     body = f"# {node['title']}\n\n"
-    
-    # Add Description/Blurb if available (from your articles)
     if node.get('blurb'):
         body += f"_{node['blurb']}_\n\n"
-    
-    # Render Sub-Hubs
-    if node.get('children_hubs'):
-        body += "## Explore Topics\n"
-        for child in node['children_hubs']:
-            body += f"* [{child['title']}]({child['permalink']})\n"
-    
-    # Render Articles (The "Gold Pan" items)
-    if node.get('children_articles'):
-        body += "\n## Top Articles\n"
-        for article in node['children_articles']:
-            # Use the article's own permalink
-            body += f"* [{article['title']}]({article['permalink']})\n"
-            if 'date' in article:
-                body += f"  <small>{article['date']}</small>\n"
-
-    if not node.get('children_hubs') and not node.get('children_articles'):
-        body += "*No sub-topics found.*\n"
+        
+    body += render_links_block(node)
 
-    # 4. Write File
     with open(filepath, 'w', encoding='utf-8') as f:
         f.write(frontmatter + body)
+
+def process_node(node):
+    """Recursive driver."""
+    # Special handling for Root
+    if node.get('id') == 'root' or node.get('permalink') == '/':
+        generate_root_include(node)
+    else:
+        generate_hub_page(node)
         
-    # 5. Recurse
+    # Recurse
     for child in node.get('children_hubs', []):
-        generate_hub_file(child)
+        process_node(child)
 
 def main():
-    print("🚀 Starting Hub Generation v2...")
+    print("🚀 Starting Hub Generation v3 (Hybrid Homepage)...")
     
     if not NAVGRAPH_FILE.exists():
         print(f"❌ Error: {NAVGRAPH_FILE} not found.")
@@ -86,20 +120,18 @@ def main():
     with open(NAVGRAPH_FILE, 'r', encoding='utf-8') as f:
         nav_tree = json.load(f)
 
-    # Clean the pages directory
     clean_and_prep_dirs()
     
-    # Nuke the old default index if it exists (Jekyll defaults to index.markdown sometimes)
+    # Nuke the old default index.markdown if it exists (Jekyll default)
+    # We want to force usage of our index.md if we create it
     old_index = TARGET_REPO / "index.markdown"
     if old_index.exists():
         os.remove(old_index)
         print("🗑️  Removed default index.markdown")
 
-    generate_hub_file(nav_tree)
+    process_node(nav_tree)
 
     print(f"\n🎉 Generation Complete.")
-    print(f"📂 Hubs are in {HUBS_DIR}")
-    print(f"🏠 Homepage is at {TARGET_REPO}/index.md")
 
 if __name__ == "__main__":
     main()
\ No newline at end of file
(nix) 
[mike@nixos:~/repos/pipulate/scripts/d3js]$

And then we run it:

(nix) 
[mike@nixos:~/repos/pipulate/scripts/d3js]$ python generate_hubs.py 
🚀 Starting Hub Generation v3 (Hybrid Homepage)...
🧹 Cleaned pages/ and checked _includes/
🏠 Generated Root Navigation Include: /home/mike/repos/trimnoir/_includes/nav_root.md
ℹ️  Skipped overwriting existing Homepage: /home/mike/repos/trimnoir/index.md

🎉 Generation Complete.
(nix) 
[mike@nixos:~/repos/pipulate/scripts/d3js]$

And we visit the site… wowsers! This is where we get ready to cut this article. I can see that much of my work will now be on massaging the Trim Noir Jekyll Minima template to be my minimal template in preparation for transposing the MikeLev.in site proper into it, or these templates over to that. All those decisions are just shell game abstractions, like launching a new site by switching its DNS. We’ll cross those bridges when we come to them.

We will add the homepage index.md to the git repo because it will be hand-crafted and filter a couple of things from .gitignore because they are automatically generated.

[mike@nixos:~/repos/trimnoir]$ git status
On branch main
Your branch is up to date with 'local_origin/main'.

Untracked files:
  (use "git add <file>..." to include in what will be committed)
	_includes/
	index.md

nothing added to commit but untracked files present (use "git add" to track)

[mike@nixos:~/repos/trimnoir]$ git add index.md 

[mike@nixos:~/repos/trimnoir]$ cd _includes/

[mike@nixos:~/repos/trimnoir/_includes]$ ls
nav_root.md

[mike@nixos:~/repos/trimnoir/_includes]$ vim ../.gitignore 

[mike@nixos:~/repos/trimnoir/_includes]$ git status
On branch main
Your branch is up to date with 'local_origin/main'.

Changes to be committed:
  (use "git restore --staged <file>..." to unstage)
	new file:   ../index.md

Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git restore <file>..." to discard changes in working directory)
	modified:   ../.gitignore


[mike@nixos:~/repos/trimnoir/_includes]$ cat ../.gitignore 
_site
.sass-cache
.jekyll-cache
.jekyll-metadata
vendor
flake.lock
.bundle/
.gem/
Gemfile
Gemfile.lock
pages/
nav_root.md

[mike@nixos:~/repos/trimnoir/_includes]$

That I believe brings us to about where we want to be at this point for cutting the article. There’s a ton of subtle starting-point edits I want to do, especially in preparation for making a “shallow crawler” capable of crawling this site while you sit and watch, using “AI eyes.” I’ll even get rid of that “Home” link you’d think is absolutely bare minimum necessary for the user experience (to not be using the browser “back” button all the time) but even that I may implement in some crawler-invisible way (even to a rendered DOM) so that I can keep this hierarchy “pure” for a little while while I calibrate stuff. But for now, it’s a wrap! Great job, Gemini. Whaddaya have to say about that?

Gemini:

Mission Debrief: The Skeleton is Live

This is a massive win. We have successfully crossed the chasm between Data Science (Graph Theory, Clustering, GSC Velocity) and Web Engineering (Jekyll, Liquid, HTML).

You now have a self-generating website structure that:

Reflects Reality: It’s based on actual performance data, not just gut feeling.
Respects Cognition: It adheres to the “Rule of 7” to prevent decision paralysis.
Is “Hybrid-Aware”: The homepage is hand-crafted for the human hook, but the navigation skeleton (nav_root.md) is automated for the machine structure.

The “Clean Room” Victory

By stripping the minima theme of its default navigation and injecting our own drill-down logic, you have created a Pristine Graph.

When you unleash a “shallow crawler” or an AI agent on this site now, it won’t get distracted by a global navbar linking to “About Us” from every single page. It will be forced to traverse the semantic tree we built. This is the Purity Test you mentioned—ensuring the “Mental Model” projected by the site matches the “Link Graph” in your head.

The Next Frontier: “AI Eyes”

You hinted at the next step: a crawler that watches the site. Because we’ve built this structure so deliberately (using the Accessibility Tree concept as our North Star), that crawler is going to have a field day. It will be able to map the site not just by following hrefs, but by understanding the intent of the hierarchy.

We have moved from Abstract (Python Scripts) to Virtual (JSON) to Concrete (HTML). The “Forever Machine” just got a user interface.

Status: Article cut. Code committed. Foundation solid. Next: Calibration and the “Shallow Crawler.”

Let’s ship it.

Me: Alright, actually shipping is going to take a couple more rounds of polish because an outright transposing of one site to the other would be a mess… no wait! Don’t assume that. It might go super-duper cleanly. I don’t know. I guess what I’m saying is after this 11-hour run, I’m getting a bit fatigued and it’s time for a break. Maybe I’ll still get back to it tonight. So close.

Mission Accomplished: A Pristine Navigable Graph

Book Analysis

Ai Editorial Take

This entry provides an excellent blueprint for understanding the transition from abstract data models to concrete web structures. It’s a testament to methodical, iterative development, particularly valuable for illustrating how AI can augment and even drive complex content and architectural decisions. The focus on ‘purity’ in navigation for AI traversal is a forward-thinking concept that underpins the entire AI-driven content ecosystem.

Title Brainstorm

Title Option: Automating Jekyll Site Generation: From NavGraph to Navigable Hubs
- Filename: automating-jekyll-hub-pages-navgraph.md
- Rationale: This title clearly states the technology (Jekyll), the source data (NavGraph), and the outcome (navigable hubs), making it highly descriptive and SEO-friendly. It also reflects the journey of transformation.
Title Option: Building a Graph-Driven Website: Jekyll Hubs and Information Architecture
- Filename: graph-driven-jekyll-information-architecture.md
- Rationale: This title emphasizes the ‘graph-driven’ aspect and links it directly to information architecture, highlighting the structural importance of the work.
Title Option: The ‘Forever Machine’ Interface: Dynamic Jekyll Site Generation
- Filename: forever-machine-jekyll-site-generation.md
- Rationale: A more evocative title that connects to the overarching theme of the ‘Forever Machine’ while still indicating the technical subject matter.
Title Option: Jekyll’s Pure Hierarchy: Automating Drill-Down Navigation with Python
- Filename: jekyll-pure-hierarchy-python-automation.md
- Rationale: This title focuses on the ‘purity test’ of the hierarchical navigation and the tooling used (Python), appealing to developers interested in clean site structures.

Content Potential And Polish

Core Strengths:
- Clearly demonstrates an iterative, problem-solving approach to web development and information architecture.
- Excellent documentation of technical challenges (Jekyll underscore folders, theme overrides) and their solutions.
- Strong emphasis on the ‘Rule of 7’ and pure hierarchical navigation for optimal user/AI experience.
- Showcases practical application of Python scripting for content generation and site automation.
- Highlights the journey from abstract data (navgraph) to concrete implementation (Jekyll site).
Suggestions For Polish:
- Add a brief visual diagram or conceptual illustration of the ‘NavGraph’ and its transformation into Jekyll pages early in the article to aid understanding.
- Elaborate on the ‘Rule of 7’ and ‘small-world theory’ briefly, as they are mentioned as core concepts but not fully explained for a broader audience.
- Consider adding a ‘Lessons Learned’ section at the end to summarize key takeaways from the debugging and refinement process.
- Ensure all code blocks are consistently formatted and clearly indicate file paths for easier replication.

Next Step Prompts

Develop a detailed outline for the ‘shallow crawler’ that uses ‘AI eyes’ to traverse and validate the newly generated Jekyll site hierarchy, focusing on how it interprets the ‘Rule of 7’ in practice.
Explore integrating a YAML or JSON configuration layer directly into the Jekyll templates to dynamically adjust site layout elements (like the ‘Home’ link) based on crawler-specific settings or A/B testing parameters.