Fix review issues: corrupted checksums, var ordering, stale links

Review fixes from 4-agent code review:

- setup.js: Handle corrupted checksums JSON gracefully (try/catch)
- setup.js: Generate checksums from source, not destination on fresh install
- setup.js: Use regex with /g flag in expandVars for multiple occurrences
- setup.sh: Fix variable ordering — set CODEFORGE_DIR before CONFIG_SOURCE_DIR
- setup.sh: Unset CONFIG_SOURCE_DIR after deprecation guard fires
- .gitignore: Remove duplicate .devcontainer/ un-ignore and stale config paths
- architecture.md: Add missing orchestrator-system-prompt.md and migration step
- README.md: Fix dead links to removed docs/ directory, point to docs site

Author: AnExiledDev

.devcontainer/README.md

@@ -432,7 +432,7 @@ The `setup-projects.sh` script auto-detects projects under `/workspaces/` and ma
 
 ## Troubleshooting
 
-Common issues and solutions. For detailed troubleshooting, see [docs/troubleshooting.md](docs/troubleshooting.md).
+Common issues and solutions. For detailed troubleshooting, see the [Troubleshooting](https://anexileddev.github.io/CodeForge/reference/troubleshooting/) page on the docs site.
 
 | Problem | Solution |
 |---------|----------|
@@ -447,11 +447,11 @@ Common issues and solutions. For detailed troubleshooting, see [docs/troubleshoo
 ## Further Reading
 
 **CodeForge Documentation**:
-- [Configuration Reference](docs/configuration-reference.md) — all env vars and config options
-- [Plugin System](docs/plugins.md) — plugin architecture and per-plugin docs
-- [Optional Features](docs/optional-features.md) — mcp-qdrant and other optional components, disabling features
-- [Keybinding Customization](docs/keybindings.md) — resolving VS Code conflicts
-- [Troubleshooting](docs/troubleshooting.md) — common issues and solutions
+- [Configuration Reference](https://anexileddev.github.io/CodeForge/customization/configuration/) — all env vars and config options
+- [Plugin System](https://anexileddev.github.io/CodeForge/plugins/) — plugin architecture and per-plugin docs
+- [Optional Features](https://anexileddev.github.io/CodeForge/customization/optional-features/) — mcp-qdrant and other optional components, disabling features
+- [Keybinding Customization](https://anexileddev.github.io/CodeForge/customization/keybindings/) — resolving VS Code conflicts
+- [Troubleshooting](https://anexileddev.github.io/CodeForge/reference/troubleshooting/) — common issues and solutions
 
 **External**:
 - [Claude Code Documentation](https://docs.anthropic.com/en/docs/claude-code)

.devcontainer/scripts/setup.sh

@@ -47,6 +47,7 @@ if [ "$CONFIG_SOURCE_DIR" = "$DEVCONTAINER_DIR/config" ] || [ "$CONFIG_SOURCE_DI
     echo "[setup] WARNING: CONFIG_SOURCE_DIR pointing to .devcontainer/config is deprecated (moved to .codeforge in v2.0)"
     echo "[setup]   Redirecting to .codeforge."
     CODEFORGE_DIR="${WORKSPACE_ROOT:?}/.codeforge"
+    unset CONFIG_SOURCE_DIR
     if [ -f "$ENV_FILE" ]; then
         sed -i 's|^CONFIG_SOURCE_DIR=.*\.devcontainer/config.*|# CONFIG_SOURCE_DIR removed (v2.0: now uses .codeforge)|' "$ENV_FILE"
         echo "[setup]   .env updated — CONFIG_SOURCE_DIR line commented out."
@@ -55,8 +56,8 @@ fi
 
 # Apply defaults for any unset variables
 : "${CLAUDE_CONFIG_DIR:=$HOME/.claude}"
-: "${CONFIG_SOURCE_DIR:=$DEVCONTAINER_DIR/config}"
 : "${CODEFORGE_DIR:=${WORKSPACE_ROOT:?}/.codeforge}"
+: "${CONFIG_SOURCE_DIR:=$CODEFORGE_DIR}"
 : "${SETUP_CONFIG:=true}"
 : "${SETUP_ALIASES:=true}"
 : "${SETUP_AUTH:=true}"

.gitignore

@@ -67,8 +67,6 @@ node_modules/
 .*
 !.devcontainer/
 !.devcontainer/**/.claude-plugin/
-!.devcontainer/
-!.devcontainer/**/.claude-plugin/**/.claude-plugin/
 !.codeforge/
 !.git/
 !.github/
@@ -81,8 +79,6 @@ node_modules/
 .codeforge/.markers/
 # Un-ignore .codeforge-preserve (user-editable, should be tracked)
 !.codeforge/.codeforge-preserve
-.devcontainer/config/claude/output-styles/strict-development.md
-.devcontainer/config/claude/mcp.json
 
 # Docs
 docs/node_modules/

docs/src/content/docs/reference/architecture.md

@@ -161,6 +161,7 @@ CodeForge ships 38 skills across the skill-engine, spec-workflow, ticket-workflo
 |   +-- settings.json              # Claude Code settings (model, plugins, env vars)
 |   +-- keybindings.json           # Keyboard shortcuts
 |   +-- main-system-prompt.md      # Development system prompt
+|   +-- orchestrator-system-prompt.md  # Orchestrator mode system prompt
 |   +-- writing-system-prompt.md   # Writing mode system prompt
 |   +-- rules/                     # Default rules deployed to .claude/rules/
 |       +-- spec-workflow.md
@@ -206,14 +207,15 @@ devcontainer.json
      |
      v
 [postStartCommand] setup.sh orchestrates:
-  1. setup-migrate-claude.sh -- Migrate Claude config from old location
-  2. setup-auth.sh           -- Git/NPM authentication
-  3. setup-config.sh         -- Deploy settings, prompts, rules via file-manifest.json
-  4. setup-aliases.sh        -- Write shell aliases to .bashrc/.zshrc
-  5. setup-plugins.sh        -- Sync plugins from marketplace
-  6. setup-projects.sh       -- Detect projects, configure Project Manager
-  7. setup-terminal.sh       -- Configure terminal settings
-  8. setup-update-claude.sh  -- Update Claude Code if needed (background)
+  1. setup-migrate-claude.sh    -- Migrate Claude config from old location
+  2. setup-migrate-codeforge.sh -- Migrate legacy config to .codeforge/
+  3. setup-auth.sh              -- Git/NPM authentication
+  4. setup-config.sh            -- Deploy settings, prompts, rules via file-manifest.json
+  5. setup-aliases.sh           -- Write shell aliases to .bashrc/.zshrc
+  6. setup-plugins.sh           -- Sync plugins from marketplace
+  7. setup-projects.sh          -- Detect projects, configure Project Manager
+  8. setup-terminal.sh          -- Configure terminal settings
+  9. setup-update-claude.sh     -- Update Claude Code if needed (background)
 ```
 
 ### Session Lifecycle

setup.js

@@ -125,7 +125,18 @@ function readChecksums(codeforgeDir) {
 	}
 
 	const latest = files[files.length - 1];
-	return JSON.parse(fs.readFileSync(path.join(checksumsDir, latest), "utf-8"));
+	try {
+		return JSON.parse(
+			fs.readFileSync(path.join(checksumsDir, latest), "utf-8"),
+		);
+	} catch {
+		console.log(
+			"  Warning: Could not read checksums from " +
+				latest +
+				", treating as fresh install.",
+		);
+		return { files: {} };
+	}
 }
 
 // ── syncCodeforgeDirectory ───────────────────────────────────────
@@ -447,7 +458,7 @@ function main() {
 
 			if (fs.existsSync(codeforgeSrc)) {
 				copyDirectory(codeforgeSrc, codeforgeDest);
-				const checksums = generateChecksums(codeforgeDest);
+				const checksums = generateChecksums(codeforgeSrc);
 				writeChecksums(codeforgeDest, packageVersion, checksums);
 			}
 
@@ -483,9 +494,9 @@ function configApply() {
 
 	function expandVars(val) {
 		return val
-			.replace("${CLAUDE_CONFIG_DIR}", claudeConfigDir)
-			.replace("${WORKSPACE_ROOT}", workspaceRoot)
-			.replace("${HOME}", process.env.HOME || "/home/vscode");
+			.replace(/\$\{CLAUDE_CONFIG_DIR\}/g, claudeConfigDir)
+			.replace(/\$\{WORKSPACE_ROOT\}/g, workspaceRoot)
+			.replace(/\$\{HOME\}/g, process.env.HOME || "/home/vscode");
 	}
 
 	console.log("");