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LLM Wiki

A pattern for building personal knowledge bases using LLMs.

This is an idea file, it is designed to be copy pasted to your own LLM Agent (e.g. OpenAI Codex, Claude Code, OpenCode / Pi, or etc.). Its goal is to communicate the high level idea, but your agent will build out the specifics in collaboration with you.

The core idea

Most people's experience with LLMs and documents looks like RAG: you upload a collection of files, the LLM retrieves relevant chunks at query time, and generates an answer. This works, but the LLM is rediscovering knowledge from scratch on every question. There's no accumulation. Ask a subtle question that requires synthesizing five documents, and the LLM has to find and piece together the relevant fragments every time. Nothing is built up. NotebookLM, ChatGPT file uploads, and most RAG systems work this way.

@OmerFarukOruc
OmerFarukOruc / claude.md
Last active September 11, 2026 21:57
AI Agent Workflow Orchestration Guidelines

AI Coding Agent Guidelines (claude.md)

These rules define how an AI coding agent should plan, execute, verify, communicate, and recover when working in a real codebase. Optimize for correctness, minimalism, and developer experience.


Operating Principles (Non-Negotiable)

  • Correctness over cleverness: Prefer boring, readable solutions that are easy to maintain.
  • Smallest change that works: Minimize blast radius; don't refactor adjacent code unless it meaningfully reduces risk or complexity.
@J-Moravec
J-Moravec / serve.r
Last active December 8, 2024 05:07
Implementation of a local server for static website using the R's internal httpd server.
error404 = paste0(
"<!DOCTYPE html>",
"<html lang=\"en\">",
"<head>",
" <meta charset=\"UTF-8\">",
" <meta name=\"viewport\" content=\"width=device-width, initial-scale=1.0\">",
" <title>Resources not found</title>",
"</head>",
"<body>",
" <div class=\"main\">",
@kmboehm
kmboehm / analyze_nuclei.py
Last active August 1, 2025 12:09
Analyze HoverNet outputs
import pandas as pd
import torch
import h5py
from openslide import OpenSlide
import os
import numpy as np
from joblib import Parallel, delayed
from features import extract_features_single_tile
import json
from scipy.stats import mannwhitneyu
@hrbrmstr
hrbrmstr / webr-experiments.R
Created April 8, 2023 10:50
Janky R script to create the HTML page for https://rud.is/webr-experiments/
#!/usr/bin/env Rscript
library(httr, include.only = c("GET", "add_headers", "content"))
library(jsonlite, include.only = c("fromJSON", "write_json"))
library(glue, include.only = c("glue"))
GITHUB_TOKEN <- Sys.getenv("GITHUB_TOKEN")
JSON_FILE <- "webr-experiments.json"
HTML_FILE <- "webr-experiments/index.html"
@AlbertRapp
AlbertRapp / connected_ggiraph.R
Created January 25, 2023 19:39
connected_ggiraph.R
library(dplyr)
library(ggplot2)
library(patchwork)
library(ggiraph)
dat <- gapminder::gapminder |>
janitor::clean_names() |>
mutate(
# ID that is shared for boxplots (this one uses factors, i.e. numbers, as ID instead of continents)
@krlmlr
krlmlr / block.R
Created June 10, 2021 03:40
Block assigning to a variable more than once
`<-` <- function(lhs, rhs, envir = parent.frame()) {
assign(as.character(substitute(lhs)), rhs, envir)
lockBinding(substitute(lhs), envir)
invisible(rhs)
}
<?php
/**
* This recipe will redirect you to the levels page after registration
*
* You can add this recipe to your site by creating a custom plugin
* or using the Code Snippets plugin available for free in the WordPress repository.
* Read this companion article for step-by-step directions on either method.
* https://www.paidmembershipspro.com/create-a-plugin-for-pmpro-customizations/
*/
function my_pmpro_redirect_after_register( $user_id ){
@domenicrosati
domenicrosati / citations_to_retracted_by_journal.csv
Created October 29, 2020 18:51
Journal Citations to Retracted Articles Post Retraction
Journal Total Citations Citations to Retracted Articles Post Retraction % of citations to retracted articles
plos one 12783331 2959 0.02%
scientific reports 6295134 1227 0.02%
oncology letters 802286 898 0.11%
journal of biological chemistry 10712422 866 0.01%
biomed research international 1789456 806 0.05%
oncotarget 1353740 791 0.06%
international journal of molecular sciences 2380553 766 0.03%
proceedings of the national academy of sciences 9984417 704 0.01%
molecular medicine reports 754664 646 0.09%
@z3tt
z3tt / github.R
Last active May 22, 2026 09:23
Configure GitHub for Rstudio
#### 1. Sign up at GitHub.com ################################################
## If you do not have a GitHub account, sign up here:
## https://github.com/join
# ----------------------------------------------------------------------------
#### 2. Install git ##########################################################
## If you do not have git installed, please do so: