refactor(naming): remove @ prefix from on-disk filenames (#131)

* refactor(naming): remove @ prefix from on-disk filenames

BREAKING CHANGE: Renames @fix_plan.md → fix_plan.md and @AGENT.md → AGENT.md

This change improves POSIX compliance and compatibility with command-line tools.
The @ prefix was originally used to avoid naming conflicts, but with the .ralph/
folder structure introduced in v0.10.0, this convention is no longer necessary.

Changes:
- Update all scripts to use new naming (fix_plan.md, AGENT.md)
- Update migration script to handle both old and new naming conventions
- Update templates to use new naming
- Update all documentation references
- Update all 420 tests to expect new naming (TDD approach)

Migration:
- Existing projects with @-prefixed files will be automatically renamed
  when running ralph-migrate
- Projects already using the new naming will continue to work unchanged

* docs(claude): update file naming conventions section

* fix(migrate): prevent orphaned @-prefixed files during migration

When both root/@fix_plan.md and .ralph/@fix_plan.md exist, the root file
now takes priority and the .ralph/@fix_plan.md is removed (backup exists).
This prevents orphaned legacy files after migration.

---------

Co-authored-by: Test User <test@example.com>

docs/archive/2025-10-milestones/EXPERT_PANEL_REVIEW.md

@@ -88,7 +88,7 @@ Loop 1-10: Normal (CLOSED state, progress detected)
 Loop 11-13: No file changes detected (transition to HALF-OPEN)
 Loop 14: Still no progress (transition to OPEN, halt execution)
 Output: "⚠️  Circuit breaker opened: No progress detected in 4 loops.
-         Last file change: loop #10. Please review @fix_plan.md."
+         Last file change: loop #10. Please review fix_plan.md."
 
 RECOMMENDATION:
 Implement Circuit Breaker with these triggers:
@@ -173,7 +173,7 @@ IMPACT: Makes Ralph's outputs parseable and actionable
 
 From PROMPT.md lines 38-45:
 "If you believe the project is complete or nearly complete:
- - Update @fix_plan.md to reflect completion status"
+ - Update fix_plan.md to reflect completion status"
 
 This requirement violates SMART criteria:
 - Specific: ❌ "believe" is subjective
@@ -183,10 +183,10 @@ This requirement violates SMART criteria:
 - Timely: ❌ No timeframe
 
 Better requirement:
-"When all tasks in @fix_plan.md are marked [x] AND no errors are present
+"When all tasks in fix_plan.md are marked [x] AND no errors are present
  in the last test run AND you have nothing left to implement from specs/:
  - Output: EXIT_SIGNAL=true
- - Update @fix_plan.md with completion summary
+ - Update fix_plan.md with completion summary
  - List any deferred items in ## Deferred section"
 
 This is:
@@ -232,7 +232,7 @@ Current state: Abstract instructions
 Required state: Concrete examples
 
 Example 1: Successful Completion
-Given: All @fix_plan.md items are checked [x]
+Given: All fix_plan.md items are checked [x]
   And: Last test run shows 100% passing
   And: No errors in logs/
 When: Claude evaluates project status
@@ -334,7 +334,7 @@ Extensions (Error Handling):
     2. Ralph exits with "no_progress" signal
 
 RECOMMENDATION:
-Document use cases in @AGENT.md or new USE_CASES.md file.
+Document use cases in AGENT.md or new USE_CASES.md file.
 Define all actors, goals, success criteria, and failure modes.
 This provides design clarity and testing scenarios.
 

docs/archive/2025-10-milestones/PHASE1_COMPLETION.md

@@ -106,7 +106,7 @@ RECOMMENDATION: <one line summary>
 
 **Clear Exit Criteria**:
 Claude sets `EXIT_SIGNAL: true` only when ALL conditions met:
-1. All @fix_plan.md items marked [x]
+1. All fix_plan.md items marked [x]
 2. All tests passing (or no tests needed)
 3. No errors/warnings in last execution
 4. All specs/ requirements implemented

docs/archive/2025-10-milestones/PHASE2_COMPLETION.md

@@ -30,7 +30,7 @@ Successfully implemented all Phase 2 recommendations from the expert panel revie
 Six concrete scenarios using Given/When/Then format:
 
 **Scenario 1: Successful Project Completion**
-- **Given**: All @fix_plan.md items marked [x], tests passing, no errors
+- **Given**: All fix_plan.md items marked [x], tests passing, no errors
 - **Then**: OUTPUT EXIT_SIGNAL=true with COMPLETE status
 - **Ralph's Action**: Gracefully exits loop with success message
 
@@ -87,7 +87,7 @@ Six concrete scenarios using Given/When/Then format:
 #### Six Primary Use Cases
 
 **UC-1: Execute Development Loop** (Main workflow)
-- **Preconditions**: PROMPT.md exists, @fix_plan.md has tasks
+- **Preconditions**: PROMPT.md exists, fix_plan.md has tasks
 - **Success**: Task completed, files modified/committed, status tracked
 - **14-step main scenario** with extensions for:
   - Circuit breaker OPEN → halt with guidance

docs/archive/2025-10-milestones/STATUS.md

@@ -23,7 +23,7 @@
 ### ✅ 75 Tests (100% Pass)
 1. **Unit Tests** (35 tests)
    - **Rate Limiting** (15 tests): can_make_call(), increment_call_counter(), edge cases
-   - **Exit Detection** (20 tests): test saturation, done signals, completion indicators, @fix_plan.md validation, error handling
+   - **Exit Detection** (20 tests): test saturation, done signals, completion indicators, fix_plan.md validation, error handling
 
 2. **Integration Tests** (40 tests)
    - **Loop Execution** (20 tests): response analyzer detection, circuit breaker states, full loop integration, exit signal detection

docs/archive/2025-10-milestones/TEST_IMPLEMENTATION_SUMMARY.md

@@ -32,7 +32,7 @@
 
    - `tests/helpers/fixtures.bash` - Test data fixtures
      - Sample PRD documents (MD, JSON)
-     - Sample PROMPT.md, @fix_plan.md, @AGENT.md
+     - Sample PROMPT.md, fix_plan.md, AGENT.md
      - Sample status.json and progress.json
      - Sample Claude Code outputs
      - Complete test project creation
@@ -83,7 +83,7 @@ Test Categories:
   - Threshold boundaries (1, 2 indicators)
   - Project completion detection
 
-- @fix_plan.md completion (5 tests)
+- fix_plan.md completion (5 tests)
   - All items complete
   - Partial completion
   - Missing file

docs/archive/2025-10-milestones/USE_CASES.md

@@ -32,7 +32,7 @@
 - Cannot modify project requirements
 - Must respect API rate limits
 - Cannot override circuit breaker when open
-- Requires valid PROMPT.md and @fix_plan.md
+- Requires valid PROMPT.md and fix_plan.md
 
 ---
 
@@ -58,7 +58,7 @@
 **Type**: Human
 **Goal**: Initiate Ralph, review results, intervene when needed
 **Capabilities**:
-- Create PROMPT.md and @fix_plan.md
+- Create PROMPT.md and fix_plan.md
 - Start/stop Ralph execution
 - Reset circuit breaker
 - Review code changes
@@ -89,7 +89,7 @@
 **Stakeholders**: Human Developer (wants progress), Claude Code (executor)
 **Preconditions**:
 - PROMPT.md exists and is valid
-- @fix_plan.md exists with at least one task
+- fix_plan.md exists with at least one task
 - Claude Code CLI is installed and accessible
 - git repository is initialized
 
@@ -105,7 +105,7 @@
 2. Ralph checks circuit breaker state (must be CLOSED or HALF_OPEN)
 3. Ralph verifies rate limit allows execution
 4. Ralph executes Claude Code with PROMPT.md
-5. Claude Code reads @fix_plan.md and selects task
+5. Claude Code reads fix_plan.md and selects task
 6. Claude Code implements task (files modified)
 7. Claude Code runs relevant tests
 8. Claude Code outputs RALPH_STATUS block
@@ -400,7 +400,7 @@
 **Main Success Scenario**:
 1. User identifies circuit breaker opened (from ralph-monitor or logs)
 2. User reviews logs/ralph.log to understand cause
-3. User fixes underlying issue (updates @fix_plan.md, fixes error, etc.)
+3. User fixes underlying issue (updates fix_plan.md, fixes error, etc.)
 4. User runs: `ralph --reset-circuit`
 5. Ralph loads circuit_breaker.sh functions
 6. Ralph calls reset_circuit_breaker("Manual reset by user")

docs/code-review/2026-01-08-phase-1.1-modern-cli-review.md

@@ -47,7 +47,7 @@ fi
 ```
 
 **Attack Vector**:
-If `@fix_plan.md` or `.response_analysis` contains malicious content like:
+If `fix_plan.md` or `.response_analysis` contains malicious content like:
 ```
 "; rm -rf /; echo "
 ```