feat(structure): migrate Ralph files to .ralph/ subfolder (#109)

* feat(structure): migrate Ralph files to .ralph/ subfolder

BREAKING CHANGE: Ralph configuration files now live in .ralph/ subfolder

This refactoring moves all Ralph-specific files into a hidden .ralph/
directory while keeping src/ at the project root. This improves
compatibility with existing tooling and keeps the project root clean.

Changes:
- Move PROMPT.md, @fix_plan.md, @AGENT.md to .ralph/
- Move specs/, logs/, docs/generated/, examples/ to .ralph/
- Move state files (.response_analysis, .circuit_breaker_state, etc.) to .ralph/
- Keep src/ at project root (unchanged)
- Add RALPH_DIR=".ralph" configuration variable
- Add ralph-migrate command for existing projects
- Create migrate_to_ralph_folder.sh migration script
- Update all path references in scripts and tests
- Update documentation (README.md, CLAUDE.md)

New project structure:
  project/
  ├── .ralph/           # Ralph configuration
  │   ├── PROMPT.md
  │   ├── @fix_plan.md
  │   ├── @AGENT.md
  │   ├── specs/
  │   ├── logs/
  │   └── docs/generated/
  └── src/              # Source code (unchanged)

Migration: Run `ralph-migrate` in existing projects to upgrade.

All 310 tests pass (100% pass rate).

* chore: add .claude/settings.local.json to .gitignore

* fix: address code review feedback for .ralph/ subfolder structure

Fixes multiple path-related issues identified in code review:

Test fixes:
- Fix create_sample_prompt to use $RALPH_DIR/PROMPT.md in test_session_continuity.bats
- Fix result_file path to use $RALPH_DIR/.json_parse_result in test_json_parsing.bats
- Fix @fix_plan.md and .response_analysis paths in test_cli_modern.bats
- Update templates directory missing test to account for global fallback

Template fix:
- Fix @fix_plan.md reference in templates/PROMPT.md to use .ralph/ prefix

Script fixes:
- Fix PROMPT_FILE comparison in ralph_loop.sh to use $RALPH_DIR/PROMPT.md
- Fix examples migration logic in migrate_to_ralph_folder.sh (remove premature mkdir)
- Move templates directory check AFTER cd in setup.sh (was checking wrong location)
- Add template directory validation with fallback to global templates

All 310 tests pass.

* Update migrate_to_ralph_folder.sh

Co-authored-by: macroscopeapp[bot] <170038800+macroscopeapp[bot]@users.noreply.github.com>

* fix: address code review feedback for .ralph/ subfolder structure

Code Review Fixes:
- Fix test_json_parsing.bats: all result_file and session file paths now use $RALPH_DIR prefix
- Fix ralph_loop.sh help text: paths now show .ralph/.ralph_session, .ralph/.call_count, etc.
- Fix migrate_to_ralph_folder.sh:
  - Proper error handling for date command (separate local declaration)
  - Use cp -a source/. dest/ pattern to preserve dotfiles and attributes
  - Remove 2>/dev/null suppression to surface copy errors
- Update create_files.sh to use .ralph/ structure for embedded scripts
- Update .gitignore with all .ralph/ state file paths
- Add old structure detection in ralph_loop.sh with helpful migration message

Version Update:
- Bump to v0.10.0 (breaking change: structural reorganization)
- Update README.md and CLAUDE.md with new version and release notes
- Add ralph-migrate documentation to Key Commands section

All 310 tests pass.

---------

Co-authored-by: macroscopeapp[bot] <170038800+macroscopeapp[bot]@users.noreply.github.com>

tests/unit/test_session_continuity.bats

@@ -15,17 +15,18 @@ setup() {
     git config user.email "test@example.com"
     git config user.name "Test User"
 
-    # Set up environment
-    export PROMPT_FILE="PROMPT.md"
-    export LOG_DIR="logs"
-    export DOCS_DIR="docs/generated"
-    export STATUS_FILE="status.json"
-    export EXIT_SIGNALS_FILE=".exit_signals"
-    export CALL_COUNT_FILE=".call_count"
-    export TIMESTAMP_FILE=".last_reset"
-    export CLAUDE_SESSION_FILE=".claude_session_id"
-    export RALPH_SESSION_FILE=".ralph_session"
-    export RALPH_SESSION_HISTORY_FILE=".ralph_session_history"
+    # Set up environment with .ralph/ subfolder structure
+    export RALPH_DIR=".ralph"
+    export PROMPT_FILE="$RALPH_DIR/PROMPT.md"
+    export LOG_DIR="$RALPH_DIR/logs"
+    export DOCS_DIR="$RALPH_DIR/docs/generated"
+    export STATUS_FILE="$RALPH_DIR/status.json"
+    export EXIT_SIGNALS_FILE="$RALPH_DIR/.exit_signals"
+    export CALL_COUNT_FILE="$RALPH_DIR/.call_count"
+    export TIMESTAMP_FILE="$RALPH_DIR/.last_reset"
+    export CLAUDE_SESSION_FILE="$RALPH_DIR/.claude_session_id"
+    export RALPH_SESSION_FILE="$RALPH_DIR/.ralph_session"
+    export RALPH_SESSION_HISTORY_FILE="$RALPH_DIR/.ralph_session_history"
     export CLAUDE_MIN_VERSION="2.0.76"
     export CLAUDE_CODE_CMD="claude"
     export CLAUDE_USE_CONTINUE="true"
@@ -35,9 +36,9 @@ setup() {
     echo "$(date +%Y%m%d%H)" > "$TIMESTAMP_FILE"
     echo '{"test_only_loops": [], "done_signals": [], "completion_indicators": []}' > "$EXIT_SIGNALS_FILE"
 
-    # Create sample project files
-    create_sample_prompt
-    create_sample_fix_plan "@fix_plan.md" 10 3
+    # Create sample project files in .ralph/ directory
+    create_sample_prompt "$RALPH_DIR/PROMPT.md"
+    create_sample_fix_plan "$RALPH_DIR/@fix_plan.md" 10 3
 
     # Source library components
     source "${BATS_TEST_DIRNAME}/../../lib/date_utils.sh"
@@ -238,7 +239,7 @@ function_exists_in_ralph() {
 EOF
 
     run parse_json_response "$output_file"
-    local result_file=".json_parse_result"
+    local result_file="$RALPH_DIR/.json_parse_result"
 
     [[ -f "$result_file" ]]