Add CLAUDE.md and LaTeX paper, remove old papers directory

- Add CLAUDE.md with project guidance for Claude Code
- Add LaTeX/ with paper and figure generation scripts
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

CLAUDE.md

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+# CLAUDE.md
+
+This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+
+## Project Overview
+
+This is a Python implementation of Douglas Hofstadter and Melanie Mitchell's Copycat algorithm for analogical reasoning. Given a pattern like "abc → abd", it finds analogous transformations for new strings (e.g., "ppqqrr → ppqqss").
+
+## Python Environment
+
+Use Anaconda Python:
+```
+C:\Users\alexa\anaconda3\python.exe
+```
+
+## Common Commands
+
+### Run the main program
+```bash
+python main.py abc abd ppqqrr --iterations 10
+```
+Arguments: `initial modified target [--iterations N] [--seed N] [--plot]`
+
+### Run with GUI (requires matplotlib)
+```bash
+python gui.py [--seed N]
+```
+
+### Run with curses terminal UI
+```bash
+python curses_main.py abc abd xyz [--fps N] [--focus-on-slipnet] [--seed N]
+```
+
+### Run tests
+```bash
+python tests.py [distributions_file]
+```
+
+### Install as module
+```bash
+pip install -e .
+```
+
+Then use programmatically:
+```python
+from copycat import Copycat
+Copycat().run('abc', 'abd', 'ppqqrr', 10)
+```
+
+## Architecture (FARG Components)
+
+The system uses the Fluid Analogies Research Group (FARG) architecture with four main components that interact each step:
+
+### Copycat (`copycat/copycat.py`)
+Central orchestrator that coordinates the main loop. Every 5 codelets, it updates the workspace, slipnet activations, and temperature.
+
+### Slipnet (`copycat/slipnet.py`)
+A semantic network of concepts (nodes) and relationships (links). Contains:
+- Letter concepts (a-z), numbers (1-5)
+- Structural concepts: positions (leftmost, rightmost), directions (left, right)
+- Bond/group types: predecessor, successor, sameness
+- Activation spreads through the network during reasoning
+
+### Coderack (`copycat/coderack.py`)
+A probabilistic priority queue of "codelets" (small procedures). Codelets are chosen stochastically based on urgency. All codelet behaviors are implemented in `copycat/codeletMethods.py` (the largest file at ~1100 lines).
+
+### Workspace (`copycat/workspace.py`)
+The "working memory" containing:
+- Three strings: initial, modified, target (and the answer being constructed)
+- Structures built during reasoning: bonds, groups, correspondences, rules
+
+### Temperature (`copycat/temperature.py`)
+Controls randomness in decision-making. High temperature = more random exploration; low temperature = more deterministic choices. Temperature decreases as the workspace becomes more organized.
+
+## Key Workspace Structures
+
+- **Bond** (`bond.py`): Links between adjacent letters (e.g., successor relationship between 'a' and 'b')
+- **Group** (`group.py`): Collection of letters with a common bond type (e.g., "abc" as a successor group)
+- **Correspondence** (`correspondence.py`): Mapping between objects in different strings
+- **Rule** (`rule.py`): The transformation rule discovered (e.g., "replace rightmost letter with successor")
+
+## Output
+
+Results show answer frequencies and quality metrics:
+- **count**: How often Copycat chose that answer (higher = more obvious)
+- **avgtemp**: Average final temperature (lower = more elegant solution)
+- **avgtime**: Average codelets run to reach answer
+
+Logs written to `output/copycat.log`, answers saved to `output/answers.csv`.