Refactor project structure and update documentation

- Migrated data files to 'data/collection/' and 'data/decks/'.
- Moved 'card_cache.json' to 'cache/'.
- Reorganized 'collection_hydrated/' and 'deck_analysis.json' into 'output/'.
- Updated 'hydrate.py' and script defaults to match the new paths.
- Updated 'README.template.md' and 'AGENTS.template.md' templates.
- Regenerated 'README.md' and 'AGENTS.md'.

docs/templates/AGENTS.template.md

@@ -27,21 +27,24 @@ python scripts/analyze_decks.py --help
 
 ```
 ├── hydrate.py              # Main CLI - fetches card data from Scryfall
-├── card_cache.json         # Local cache of Scryfall card data
-├── deck_analysis.json      # Analysis output
-├── collection/             # Raw decklist text files
-├── collection_hydrated/    # Enriched card data by type
-│   ├── deck.json           # All cards combined
-│   ├── commander.json
-│   ├── creatures.json
-│   ├── instants.json
-│   ├── sorceries.json
-│   ├── artifacts.json
-│   ├── enchantments.json
-│   ├── lands.json
-│   └── planeswalkers.json
-├── decks/                  # Deck definitions (JSON)
-│   └── <deck_name>.json    # name, commander, colors, archetype, cards
+├── cache/
+│   └── card_cache.json     # Local cache of Scryfall card data
+├── output/
+│   ├── deck_analysis.json  # Analysis output
+│   └── hydrated/           # Enriched card data by type
+│       ├── deck.json       # All cards combined
+│       ├── commander.json
+│       ├── creatures.json
+│       ├── instants.json
+│       ├── sorceries.json
+│       ├── artifacts.json
+│       ├── enchantments.json
+│       ├── lands.json
+│       └── planeswalkers.json
+├── data/
+│   ├── collection/         # Raw decklist text files
+│   └── decks/              # Deck definitions (JSON)
+│       └── <deck_name>.json    # name, commander, colors, archetype, cards
 ├── scripts/
 │   ├── analyze_decks.py    # Find upgrade options for decks
 │   ├── find_synergies.py   # Search for synergistic cards
@@ -53,7 +56,7 @@ python scripts/analyze_decks.py --help
 
 ## Data Formats
 
-### Deck JSON (`decks/*.json`)
+### Deck JSON (`data/decks/*.json`)
 
 ```json
 {
@@ -68,7 +71,7 @@ python scripts/analyze_decks.py --help
 }
 ```
 
-### Card Data (`collection_hydrated/*.json`)
+### Card Data (`output/hydrated/*.json`)
 
 Array of card objects with Scryfall fields:
 - `name`, `mana_cost`, `cmc`, `colors`, `color_identity`
@@ -79,7 +82,7 @@ Array of card objects with Scryfall fields:
 
 ### Adding a New Deck
 
-1. Create `decks/<name>.json` with required fields
+1. Create `data/decks/<name>.json` with required fields
 2. Run `python scripts/update_docs.py` to regenerate documentation
 
 ### Adding a New Script
@@ -97,4 +100,4 @@ Array of card objects with Scryfall fields:
 
 ## Current Decks
 
-{{DECK_TABLE}}
+{{DECK_TABLE}}