Update documentation for Quarto/Devito focus

- Rewrite README.md to highlight Devito DSL and modern tooling
- Update index.qmd with Devito introduction and code example
- Update CLAUDE.md with Devito patterns and project structure
- Update _quarto.yml source URLs to point to devitocodes repo
- Remove devito-plan.md (completed development roadmap)
- Remove issues.md (conversion tracking no longer needed)

Author: ggorman

CLAUDE.md

@@ -4,7 +4,13 @@ This file provides guidance to Claude Code (claude.ai/code) when working with co
 
 ## Project Overview
 
-This is the source repository for *Finite Difference Computing with PDEs - A Modern Software Approach* by Hans Petter Langtangen and Svein Linge. The book teaches finite difference methods for solving PDEs through Python implementations.
+This is the source repository for *Finite Difference Computing with PDEs - A Modern Software Approach* by Hans Petter Langtangen and Svein Linge. The book teaches finite difference methods for solving PDEs using [Devito](https://www.devitoproject.org/), a domain-specific language for symbolic PDE specification.
+
+### Key Technologies
+
+- **Devito** - DSL for symbolic PDE specification and automatic code generation
+- **Quarto** - Scientific publishing system for HTML and PDF output
+- **SymPy** - Symbolic mathematics for derivations and verification
 
 ## Build Commands
 
@@ -19,36 +25,62 @@ quarto preview             # Live preview with hot reload
 ### Run Tests
 
 ```bash
-pytest src/                              # Run all tests
-pytest src/vib/vib.py -v                 # Run tests in specific file
-python -m pytest --tb=short              # With short traceback
+pytest tests/ -v                    # Run all tests
+pytest tests/ -v -m "not devito"    # Skip Devito tests
+pytest tests/ -v -m devito          # Devito tests only
 ```
 
 ### Linting
 
 ```bash
 ruff check src/                          # Check for linting errors
 isort --check-only src/                  # Check import ordering
-isort src/                               # Fix import ordering
 pre-commit run --all-files               # Run all pre-commit hooks
-pre-commit run --hook-stage manual       # Run auto-fix hooks
 ```
 
 ## Architecture
 
 ### Directory Structure
 
 - `chapters/` - Quarto source files organized by topic:
-  - `vib/` - Vibration ODEs
-  - `wave/` - Wave equations
-  - `diffu/` - Diffusion equations
-  - `advec/` - Advection equations
-  - `nonlin/` - Nonlinear problems
+  - `devito_intro/` - Introduction to Devito DSL
+  - `wave/` - Wave equations (includes Devito solvers)
+  - `diffu/` - Diffusion equations (includes Devito solvers)
+  - `advec/` - Advection equations (includes Devito solvers)
+  - `nonlin/` - Nonlinear problems (includes Devito solvers)
   - `appendices/` - Truncation errors, formulas, software engineering
-- `src/` - Python source code organized by chapter
+- `src/` - Python source code:
+  - `wave/` - Wave equation solvers (wave1D_devito.py, wave2D_devito.py)
+  - `diffu/` - Diffusion solvers (diffu1D_devito.py, diffu2D_devito.py)
+  - `advec/` - Advection solvers (advec1D_devito.py)
+  - `nonlin/` - Nonlinear solvers (nonlin1D_devito.py)
+  - `operators.py` - FD operators with symbolic derivation
+  - `verification.py` - Symbolic verification utilities
+- `tests/` - Pytest test suite
 - `_book/` - Generated output (PDF, HTML)
 - `_quarto.yml` - Book configuration
 
+### Devito Patterns
+
+When writing Devito code, follow these patterns:
+
+```python
+from devito import Grid, TimeFunction, Eq, Operator
+
+# 1. Create a grid
+grid = Grid(shape=(nx,), extent=(L,))
+
+# 2. Create fields
+u = TimeFunction(name='u', grid=grid, time_order=2, space_order=2)
+
+# 3. Write equations symbolically
+eq = Eq(u.forward, 2*u - u.backward + (c*dt)**2 * u.dx2)
+
+# 4. Create and apply operator
+op = Operator([eq])
+op.apply(time_M=nt, dt=dt)
+```
+
 ### Quarto Document Format
 
 The book uses [Quarto](https://quarto.org/) for scientific publishing. Key syntax:
@@ -59,10 +91,6 @@ The book uses [Quarto](https://quarto.org/) for scientific publishing. Key synta
 - `{{< include file.qmd >}}` - Include another file
 - `{=latex}` blocks for raw LaTeX when needed
 
-### Code Organization Pattern
-
-Each chapter's Python code lives in `src/CHAPTER/` and can be included in QMD files using fenced code blocks or Quarto includes.
-
 ## Pre-commit Hooks
 
 Pre-commit hooks run automatically on commit:
@@ -75,28 +103,18 @@ Pre-commit hooks run automatically on commit:
 
 ## Key Dependencies
 
+- **devito** - PDE solver DSL (optional, for running solvers)
 - **quarto** - Document generation from .qmd files
-- **numpy, scipy, matplotlib, sympy** - Scientific Python stack for examples
-- **pdflatex** - LaTeX compilation (requires TeX Live installation)
+- **numpy, scipy, matplotlib, sympy** - Scientific Python stack
+- **pdflatex** - LaTeX compilation (requires TeX Live)
 
 ## Build Output
 
 - `_book/Finite-Difference-Computing-with-PDEs.pdf` - Generated book PDF
 
 ## Quarto Equation Labeling Guidelines
 
-**Known Bug (GitHub Issue #2275)**: Quarto's `{#eq-label}` syntax cannot label individual lines within `\begin{align}` environments. This causes "macro parameter character #" LaTeX errors.
-
-### What Fails
-
-```markdown
-$$
-\begin{align}
-a &= 0+1 {#eq-first}    <!-- causes LaTeX error -->
-b &= 2+3 {#eq-second}
-\end{align}
-$$
-```
+**Known Bug (GitHub Issue #2275)**: Quarto's `{#eq-label}` syntax cannot label individual lines within `\begin{align}` environments.
 
 ### Working Patterns
 
@@ -110,36 +128,14 @@ b &= 2+3
 $$ {#eq-block}
 ```
 
-**Multiple separate equations** - use separate `$$` blocks:
-```markdown
-$$
-a = 0+1
-$$ {#eq-first}
-$$
-b = 2+3
-$$ {#eq-second}
-```
-
 **Individual line labels in align** - use pure AMS LaTeX syntax:
 ```latex
 \begin{align}
 a &= 0+1 \label{eq:first} \\
 b &= 2+3 \label{eq:second}
 \end{align}
-
-See Equation \eqref{eq:first} for details.
 ```
 
-### Best Practices
-
-- **Never mix Quarto `{#eq-}` and AMS `\label{}` syntax** in the same equation
-- Use `\begin{equation}...\end{equation}` for single numbered equations
-- Use `\begin{align}...\end{align}` with `\label{}` for multiple aligned, individually-numbered equations
-- Use `\begin{aligned}...\end{aligned}` inside `\begin{equation}` for aligned equations sharing one number
-- Add `*` (e.g., `\begin{align*}`) to suppress all numbering
-- Reference with `\eqref{label}` for parenthesized numbers, `\ref{label}` for plain numbers
-- For Quarto cross-refs, use `@eq-label` syntax with label placed after `$$`
-
 ### Cross-Reference Prefixes
 
 | Type | Prefix | Example |
@@ -148,5 +144,3 @@ See Equation \eqref{eq:first} for details.
 | Equation | `@eq-` | `@eq-vib-ode1-step4` |
 | Figure | `@fig-` | `@fig-vib-phase` |
 | Table | `@tbl-` | `@tbl-trunc-fd1` |
-
-Reference: [NMFS-OpenSci Quarto-AMS Math Guide](https://nmfs-opensci.github.io/quarto-amsmath)