fix(cli): make wmill init generated skills respect nonDottedPaths config

cli/src/commands/init/init.ts

@@ -252,6 +252,16 @@ async function initAction(opts: InitOptions) {
     }
   }
 
+  // Read nonDottedPaths from config to specialize generated skills
+  let nonDottedPaths = true; // default for new inits
+  try {
+    const { readConfigFile } = await import("../../core/conf.ts");
+    const config = await readConfigFile();
+    nonDottedPaths = config.nonDottedPaths ?? true;
+  } catch {
+    // If config can't be read, use default
+  }
+
   // Create guidance files (AGENTS.md, CLAUDE.md, and Claude skills)
   try {
     // Generate skills reference section for AGENTS.md
@@ -290,6 +300,20 @@ async function initAction(opts: InitOptions) {
 
           let skillContent = SKILL_CONTENT[skill.name];
           if (skillContent) {
+            // Replace placeholders with actual suffixes based on nonDottedPaths
+            if (nonDottedPaths) {
+              skillContent = skillContent
+                .replaceAll("{{FLOW_SUFFIX}}", "__flow")
+                .replaceAll("{{APP_SUFFIX}}", "__app")
+                .replaceAll("{{RAW_APP_SUFFIX}}", "__raw_app")
+                .replaceAll("{{INLINE_SCRIPT_NAMING}}", "Inline script files should NOT include `.inline_script.` in their names (e.g. use `a.ts`, not `a.inline_script.ts`).");
+            } else {
+              skillContent = skillContent
+                .replaceAll("{{FLOW_SUFFIX}}", ".flow")
+                .replaceAll("{{APP_SUFFIX}}", ".app")
+                .replaceAll("{{RAW_APP_SUFFIX}}", ".raw_app")
+                .replaceAll("{{INLINE_SCRIPT_NAMING}}", "Inline script files use the `.inline_script.` naming convention (e.g. `a.inline_script.ts`).");
+            }
             // Check if this skill has schemas that need to be appended
             const schemaMappings = SCHEMA_MAPPINGS[skill.name];
             if (schemaMappings && schemaMappings.length > 0) {

cli/src/guidance/skills.ts

@@ -4236,10 +4236,10 @@ description: MUST use when creating flows.
 
 ## CLI Commands
 
-Create a folder ending with \`.flow\` and add a YAML file with the flow definition.
-For rawscript modules, use \`!inline path/to/script.ts\` for the content key.
+Create a folder ending with \`{{FLOW_SUFFIX}}\` and add a \`flow.yaml\` file with the flow definition.
+For rawscript modules, use \`!inline path/to/script.ts\` for the content key. {{INLINE_SCRIPT_NAMING}}
 After writing, tell the user they can run:
-- \`wmill flow generate-locks <path_to_flow_folder> --yes\` - Generate lock files for the specific flow you modified (e.g. \`wmill flow generate-locks f/my_folder/my_flow.flow --yes\`)
+- \`wmill flow generate-locks <path_to_flow_folder> --yes\` - Generate lock files for the specific flow you modified (e.g. \`wmill flow generate-locks f/my_folder/my_flow{{FLOW_SUFFIX}} --yes\`)
 - \`wmill sync push\` - Deploy to Windmill
 
 Do NOT run these commands yourself. Instead, inform the user that they should run them.
@@ -4375,7 +4375,7 @@ This interactive command creates a complete app structure with your choice of fr
 ## App Structure
 
 \`\`\`
-my_app.raw_app/
+my_app{{RAW_APP_SUFFIX}}/
 ├── AGENTS.md              # AI agent instructions (auto-generated)
 ├── DATATABLES.md          # Database schemas (run 'wmill app generate-agents' to refresh)
 ├── raw_app.yaml           # App configuration (summary, path, data settings)

system_prompts/auto-generated/flow.md

@@ -2,10 +2,10 @@
 
 ## CLI Commands
 
-Create a folder ending with `.flow` and add a YAML file with the flow definition.
-For rawscript modules, use `!inline path/to/script.ts` for the content key.
+Create a folder ending with `__flow` and add a `flow.yaml` file with the flow definition.
+For rawscript modules, use `!inline path/to/script.ts` for the content key. Inline script files should NOT include `.inline_script.` in their names (e.g. use `a.ts`, not `a.inline_script.ts`).
 After writing, tell the user they can run:
-- `wmill flow generate-locks <path_to_flow_folder> --yes` - Generate lock files for the specific flow you modified (e.g. `wmill flow generate-locks f/my_folder/my_flow.flow --yes`)
+- `wmill flow generate-locks <path_to_flow_folder> --yes` - Generate lock files for the specific flow you modified (e.g. `wmill flow generate-locks f/my_folder/my_flow__flow --yes`)
 - `wmill sync push` - Deploy to Windmill
 
 Do NOT run these commands yourself. Instead, inform the user that they should run them.

system_prompts/auto-generated/prompts.ts

@@ -33,10 +33,10 @@ export const FLOW_BASE = `# Windmill Flow Building Guide
 
 ## CLI Commands
 
-Create a folder ending with \`.flow\` and add a YAML file with the flow definition.
-For rawscript modules, use \`!inline path/to/script.ts\` for the content key.
+Create a folder ending with \`__flow\` and add a \`flow.yaml\` file with the flow definition.
+For rawscript modules, use \`!inline path/to/script.ts\` for the content key. Inline script files should NOT include \`.inline_script.\` in their names (e.g. use \`a.ts\`, not \`a.inline_script.ts\`).
 After writing, tell the user they can run:
-- \`wmill flow generate-locks <path_to_flow_folder> --yes\` - Generate lock files for the specific flow you modified (e.g. \`wmill flow generate-locks f/my_folder/my_flow.flow --yes\`)
+- \`wmill flow generate-locks <path_to_flow_folder> --yes\` - Generate lock files for the specific flow you modified (e.g. \`wmill flow generate-locks f/my_folder/my_flow__flow --yes\`)
 - \`wmill sync push\` - Deploy to Windmill
 
 Do NOT run these commands yourself. Instead, inform the user that they should run them.

system_prompts/auto-generated/skills/raw-app/SKILL.md

@@ -18,7 +18,7 @@ This interactive command creates a complete app structure with your choice of fr
 ## App Structure
 
 ```
-my_app.raw_app/
+my_app__raw_app/
 ├── AGENTS.md              # AI agent instructions (auto-generated)
 ├── DATATABLES.md          # Database schemas (run 'wmill app generate-agents' to refresh)
 ├── raw_app.yaml           # App configuration (summary, path, data settings)

system_prompts/auto-generated/skills/write-flow/SKILL.md

@@ -7,10 +7,10 @@ description: MUST use when creating flows.
 
 ## CLI Commands
 
-Create a folder ending with `.flow` and add a YAML file with the flow definition.
-For rawscript modules, use `!inline path/to/script.ts` for the content key.
+Create a folder ending with `__flow` and add a `flow.yaml` file with the flow definition.
+For rawscript modules, use `!inline path/to/script.ts` for the content key. Inline script files should NOT include `.inline_script.` in their names (e.g. use `a.ts`, not `a.inline_script.ts`).
 After writing, tell the user they can run:
-- `wmill flow generate-locks <path_to_flow_folder> --yes` - Generate lock files for the specific flow you modified (e.g. `wmill flow generate-locks f/my_folder/my_flow.flow --yes`)
+- `wmill flow generate-locks <path_to_flow_folder> --yes` - Generate lock files for the specific flow you modified (e.g. `wmill flow generate-locks f/my_folder/my_flow__flow --yes`)
 - `wmill sync push` - Deploy to Windmill
 
 Do NOT run these commands yourself. Instead, inform the user that they should run them.

system_prompts/base/flow-base.md

@@ -2,10 +2,10 @@
 
 ## CLI Commands
 
-Create a folder ending with `.flow` and add a YAML file with the flow definition.
-For rawscript modules, use `!inline path/to/script.ts` for the content key.
+Create a folder ending with `__flow` and add a `flow.yaml` file with the flow definition.
+For rawscript modules, use `!inline path/to/script.ts` for the content key. Inline script files should NOT include `.inline_script.` in their names (e.g. use `a.ts`, not `a.inline_script.ts`).
 After writing, tell the user they can run:
-- `wmill flow generate-locks <path_to_flow_folder> --yes` - Generate lock files for the specific flow you modified (e.g. `wmill flow generate-locks f/my_folder/my_flow.flow --yes`)
+- `wmill flow generate-locks <path_to_flow_folder> --yes` - Generate lock files for the specific flow you modified (e.g. `wmill flow generate-locks f/my_folder/my_flow__flow --yes`)
 - `wmill sync push` - Deploy to Windmill
 
 Do NOT run these commands yourself. Instead, inform the user that they should run them.

system_prompts/base/raw-app.md

@@ -13,7 +13,7 @@ This interactive command creates a complete app structure with your choice of fr
 ## App Structure
 
 ```
-my_app.raw_app/
+my_app__raw_app/
 ├── AGENTS.md              # AI agent instructions (auto-generated)
 ├── DATATABLES.md          # Database schemas (run 'wmill app generate-agents' to refresh)
 ├── raw_app.yaml           # App configuration (summary, path, data settings)

system_prompts/generate.py

@@ -1094,6 +1094,20 @@ def main():
 
     # Generate skills TypeScript export for CLI
     skills_ts = generate_skills_ts_export(skills, schema_yaml_content)
+
+    # Replace hardcoded path conventions with placeholders for CLI runtime resolution.
+    # init.ts resolves these based on the nonDottedPaths setting in wmill.yaml.
+    # (Frontend auto-generated files keep the default non-dotted conventions.)
+    skills_ts = (skills_ts
+        .replace("\\`__flow\\`", "\\`{{FLOW_SUFFIX}}\\`")
+        .replace(
+            "Inline script files should NOT include \\`.inline_script.\\`"
+            " in their names (e.g. use \\`a.ts\\`, not \\`a.inline_script.ts\\`).",
+            "{{INLINE_SCRIPT_NAMING}}"
+        )
+        .replace("my_flow__flow", "my_flow{{FLOW_SUFFIX}}")
+        .replace("my_app__raw_app/", "my_app{{RAW_APP_SUFFIX}}/")
+    )
     (CLI_GUIDANCE_DIR / "skills.ts").write_text(skills_ts)
 
     print(f"\nGenerated files:")