feat: Add cobol-source folder in root and update all references

- Create cobol-source/ directory in root as static folder for COBOL files
- Add cobol-source/.gitkeep to preserve directory in git
- Update all documentation to reference cobol-source/ instead of source/
- Update doctor.sh commands to use ./cobol-source
- Update .gitignore to ignore cobol-source/* (except .gitkeep)
- Update default COBOL_SOURCE_FOLDER config to 'cobol-source'
- Keep backward compatibility with source/ folder

Author: gkaleta

.devcontainer/README.md

@@ -152,8 +152,10 @@ Once running, access these URLs:
 ├── Data/                    # SQLite database
 │   └── migration.db         # Migration metadata
 ├── Logs/                    # Migration logs
-├── cobol-source/            # Input COBOL files
-├── java-output/             # Generated Java code
+├── cobol-source/            # Input COBOL files (YOUR COBOL FILES GO HERE)
+├── output/
+│   ├── java-output/         # Generated Java code
+│   └── dotnet-output/       # Generated .NET code
 ├── McpChatWeb/              # Web portal project
 │   └── wwwroot/             # Frontend files
 ├── Config/                  # Configuration files

.gitignore

@@ -81,6 +81,8 @@ Config/appsettings.secrets.json
 # =============================================================================
 
 # COBOL Source Files (Contains proprietary business logic)
+cobol-source/*
+!cobol-source/.gitkeep
 source/*
 !source/.gitkeep
 cobol-files/

QUICK_START.md

@@ -308,7 +308,7 @@ Now that you're set up, explore these areas:
 
 1. **Run a Full Migration:**
    ```bash
-   # Place COBOL files in source/
+   # Place COBOL files in cobol-source/
    ./doctor.sh run
    ```
 

README.md

@@ -622,7 +622,7 @@ dotnet run conversation
 ## Step-by-Step Guide
 
 1. **Configure:** `cp Config/ai-config.local.env.example Config/ai-config.local.env` → Add Azure OpenAI endpoint, API key, deployment name
-2. **Add COBOL files:** `cp your-files/* ./source/`
+2. **Add COBOL files:** `cp your-files/* ./cobol-source/`
 3. **Run:** `./doctor.sh run` - Analyzes, converts, launches portal at http://localhost:5250
 4. **Explore:** Use portal UI (chat, graph) or connect MCP clients (Claude, Cursor)
 5. **Query data:** SQLite (`Data/migration.db`), Neo4j (http://localhost:7474), or MCP API

cobol-source/.gitkeep

@@ -610,8 +610,8 @@ run_test() {
     # Check source folders
     echo ""
     echo "Checking source folders..."
-    cobol_files=$(find "$REPO_ROOT/source" -name "*.cbl" 2>/dev/null | wc -l)
-    copybook_files=$(find "$REPO_ROOT/source" -name "*.cpy" 2>/dev/null | wc -l)
+    cobol_files=$(find "$REPO_ROOT/cobol-source" -name "*.cbl" 2>/dev/null | wc -l)
+    copybook_files=$(find "$REPO_ROOT/cobol-source" -name "*.cpy" 2>/dev/null | wc -l)
     total_files=$((cobol_files + copybook_files))
 
     if [ "$total_files" -gt 0 ]; then
@@ -623,7 +623,7 @@ run_test() {
         fi
     else
         echo -e "${YELLOW}⚠️  No COBOL files or copybooks found in source directory${NC}"
-        echo "   Add your COBOL files to ./source/ to test migration"
+        echo "   Add your COBOL files to ./cobol-source/ to test migration"
     fi
 
     # Check output directories
@@ -681,14 +681,14 @@ run_test() {
     echo ""
     echo "Migration Options:"
     echo "  Standard:         ./doctor.sh run"
-    echo "  Reverse Engineer: dotnet run reverse-engineer --source ./source"
-    echo "  Full Migration:   dotnet run -- --source ./source"
+    echo "  Reverse Engineer: dotnet run reverse-engineer --source ./cobol-source"
+    echo "  Full Migration:   dotnet run -- --source ./cobol-source"
     echo ""
     if [ $re_components -eq $re_components_total ]; then
         echo "Reverse Engineering Available:"
         echo "  Extract business logic from COBOL before migration"
         echo "  Generate documentation in markdown format"
-        echo "  Run: dotnet run reverse-engineer --source ./source"
+        echo "  Run: dotnet run reverse-engineer --source ./cobol-source"
         echo ""
     fi
     if [ "$total_files" -gt 0 ]; then
@@ -750,7 +750,7 @@ run_migration() {
     fi
 
     # Run the application with updated folder structure
-    "$DOTNET_CMD" run -- --source ./source $skip_reverse_eng
+    "$DOTNET_CMD" run -- --source ./cobol-source $skip_reverse_eng
     local migration_exit=$?
 
     if [[ $migration_exit -ne 0 ]]; then
@@ -802,7 +802,7 @@ run_resume() {
     fi
 
     # Run with resume logic
-    "$DOTNET_CMD" run -- --source ./source --resume
+    "$DOTNET_CMD" run -- --source ./cobol-source --resume
 }
 
 # Function to monitor migration
@@ -969,12 +969,12 @@ run_reverse_engineering() {
     echo ""
 
     # Check for COBOL files
-    cobol_count=$(find "$REPO_ROOT/source" -name "*.cbl" 2>/dev/null | wc -l)
-    copybook_count=$(find "$REPO_ROOT/source" -name "*.cpy" 2>/dev/null | wc -l)
+    cobol_count=$(find "$REPO_ROOT/cobol-source" -name "*.cbl" 2>/dev/null | wc -l)
+    copybook_count=$(find "$REPO_ROOT/cobol-source" -name "*.cpy" 2>/dev/null | wc -l)
     total_count=$((cobol_count + copybook_count))
 
     if [ "$total_count" -eq 0 ]; then
-        echo -e "${YELLOW}⚠️  No COBOL files or copybooks found in ./source/${NC}"
+        echo -e "${YELLOW}⚠️  No COBOL files or copybooks found in ./cobol-source/${NC}"
         echo "Add COBOL files to analyze and try again."
         return 1
     fi
@@ -988,7 +988,7 @@ run_reverse_engineering() {
     echo ""
 
     # Run the reverse engineering command
-    "$DOTNET_CMD" run reverse-engineer --source ./source
+    "$DOTNET_CMD" run reverse-engineer --source ./cobol-source
 
     local exit_code=$?
 
@@ -1040,7 +1040,7 @@ run_conversion_only() {
     echo ""
 
     # Run the application with skip-reverse-engineering flag
-    "$DOTNET_CMD" run -- --source ./source --skip-reverse-engineering
+    "$DOTNET_CMD" run -- --source ./cobol-source --skip-reverse-engineering
     local migration_exit=$?
 
     if [[ $migration_exit -ne 0 ]]; then
@@ -1069,7 +1069,7 @@ run_conversion_only() {
 # Main command routing
 main() {
     # Create required directories if they don't exist
-    mkdir -p "$REPO_ROOT/source" "$REPO_ROOT/output" "$REPO_ROOT/Logs"
+    mkdir -p "$REPO_ROOT/cobol-source" "$REPO_ROOT/source" "$REPO_ROOT/output" "$REPO_ROOT/Logs"
 
     case "${1:-doctor}" in
         "setup")