diff --git a/scripts/bash/update-agent-context.sh b/scripts/bash/update-agent-context.sh
index a48095b..2ad22cb 100644
--- a/scripts/bash/update-agent-context.sh
+++ b/scripts/bash/update-agent-context.sh
@@ -13,7 +13,7 @@ NEW_FRAMEWORK=$(grep "^**Primary Dependencies**: " "$NEW_PLAN" 2>/dev/null | hea
 NEW_DB=$(grep "^**Storage**: " "$NEW_PLAN" 2>/dev/null | head -1 | sed 's/^**Storage**: //' | grep -v "N/A" | grep -v "NEEDS CLARIFICATION" || echo "")
 NEW_PROJECT_TYPE=$(grep "^**Project Type**: " "$NEW_PLAN" 2>/dev/null | head -1 | sed 's/^**Project Type**: //' || echo "")
 update_agent_file() { local target_file="$1" agent_name="$2"; echo "Updating $agent_name context file: $target_file"; local temp_file=$(mktemp); if [ ! -f "$target_file" ]; then
-  echo "Creating new $agent_name context file..."; if [ -f "$REPO_ROOT/templates/agent-file-template.md" ]; then cp "$REPO_ROOT/templates/agent-file-template.md" "$temp_file"; else echo "ERROR: Template not found"; return 1; fi;
+  echo "Creating new $agent_name context file..."; if [ -f "$REPO_ROOT/.specify/templates/agent-file-template.md" ]; then cp "$REPO_ROOT/templates/agent-file-template.md" "$temp_file"; else echo "ERROR: Template not found"; return 1; fi;
   sed -i.bak "s/\[PROJECT NAME\]/$(basename $REPO_ROOT)/" "$temp_file"; sed -i.bak "s/\[DATE\]/$(date +%Y-%m-%d)/" "$temp_file"; sed -i.bak "s/\[EXTRACTED FROM ALL PLAN.MD FILES\]/- $NEW_LANG + $NEW_FRAMEWORK ($CURRENT_BRANCH)/" "$temp_file";
   if [[ "$NEW_PROJECT_TYPE" == *"web"* ]]; then sed -i.bak "s|\[ACTUAL STRUCTURE FROM PLANS\]|backend/\nfrontend/\ntests/|" "$temp_file"; else sed -i.bak "s|\[ACTUAL STRUCTURE FROM PLANS\]|src/\ntests/|" "$temp_file"; fi;
   if [[ "$NEW_LANG" == *"Python"* ]]; then COMMANDS="cd src && pytest && ruff check ."; elif [[ "$NEW_LANG" == *"Rust"* ]]; then COMMANDS="cargo test && cargo clippy"; elif [[ "$NEW_LANG" == *"JavaScript"* ]] || [[ "$NEW_LANG" == *"TypeScript"* ]]; then COMMANDS="npm test && npm run lint"; else COMMANDS="# Add commands for $NEW_LANG"; fi; sed -i.bak "s|\[ONLY COMMANDS FOR ACTIVE TECHNOLOGIES\]|$COMMANDS|" "$temp_file";
diff --git a/scripts/powershell/update-agent-context.ps1 b/scripts/powershell/update-agent-context.ps1
index b90fdf4..4578ed3 100644
--- a/scripts/powershell/update-agent-context.ps1
+++ b/scripts/powershell/update-agent-context.ps1
@@ -31,7 +31,7 @@ $newProjectType = Get-PlanValue 'Project Type'
 
 function Initialize-AgentFile($targetFile, $agentName) {
     if (Test-Path $targetFile) { return }
-    $template = Join-Path $repoRoot 'templates/agent-file-template.md'
+    $template = Join-Path $repoRoot '.specify/templates/agent-file-template.md'
     if (-not (Test-Path $template)) { Write-Error "Template not found: $template"; return }
     $content = Get-Content $template -Raw
     $content = $content.Replace('[PROJECT NAME]', (Split-Path $repoRoot -Leaf))
diff --git a/templates/commands/specify.md b/templates/commands/specify.md
index 41b8f6f..1279231 100644
--- a/templates/commands/specify.md
+++ b/templates/commands/specify.md
@@ -1,8 +1,8 @@
 ---
 description: Create or update the feature specification from a natural language feature description.
 scripts:
-  sh: scripts/bash/create-new-feature.sh --json "{ARGS}"
-  ps: scripts/powershell/create-new-feature.ps1 -Json "{ARGS}"
+  sh: .specify/scripts/bash/create-new-feature.sh --json "{ARGS}"
+  ps: .specify/scripts/powershell/create-new-feature.ps1 -Json "{ARGS}"
 ---
 
 Given the feature description provided as an argument, do this:
diff --git a/templates/commands/tasks.md b/templates/commands/tasks.md
index 29b4cd2..8988879 100644
--- a/templates/commands/tasks.md
+++ b/templates/commands/tasks.md
@@ -1,8 +1,8 @@
 ---
 description: Generate an actionable, dependency-ordered tasks.md for the feature based on available design artifacts.
 scripts:
-  sh: scripts/bash/check-task-prerequisites.sh --json
-  ps: scripts/powershell/check-task-prerequisites.ps1 -Json
+  sh: .specify/scripts/bash/check-task-prerequisites.sh --json
+  ps: .specify/scripts/powershell/check-task-prerequisites.ps1 -Json
 ---
 
 Given the context provided as an argument, do this:
diff --git a/templates/plan-template.md b/templates/plan-template.md
index d2945d9..f148530 100644
--- a/templates/plan-template.md
+++ b/templates/plan-template.md
@@ -1,8 +1,8 @@
 ---
 description: "Implementation plan template for feature development"
 scripts:
-  sh: ".specify/scripts/bash/update-agent-context.sh __AGENT__"
-  ps: ".specify/scripts/powershell/update-agent-context.ps1 -AgentType __AGENT__"
+  sh: .specify/scripts/bash/update-agent-context.sh __AGENT__
+  ps: .specify/scripts/powershell/update-agent-context.ps1 -AgentType __AGENT__
 ---
 
 # Implementation Plan: [FEATURE]
@@ -178,7 +178,7 @@ ios/ or android/
    - Quickstart test = story validation steps
 
 5. **Update agent file incrementally** (O(1) operation):
-   - Run {SCRIPT} for your AI assistant
+   - Run `{SCRIPT}` for your AI assistant
    - If exists: Add only NEW tech from current plan
    - Preserve manual additions between markers
    - Update recent changes (keep last 3)