cli: prompt generation creates code file includes instead of example file includes


Using the cli, creating prompts from template generic/generate_prompt creates prompts that include the .py code file paths instead of the _example.py filepaths.

output prompt snippet:
```

Dependencies

<storage_layer>
<include>src/core/storage_layer.py</include>
</storage_layer>

Prompt Dependencies:
- `storage_layer_Python.prompt` — Provides CRUD operations, batch read/write, and query-by-staleness-status capabilities for bookmark records. The staleness review module depends on querying bookmarks by staleness classification and updating bookmark records with review decisions and URL replacements.
```


commandline:
```
pdd --strength 0.88 --local --force generate --template generic/generate_prompt -e MODULE=staleness_review -e LANG_OR_FRAMEWORK=Python -e ARCHITECTURE_FILE=architecture.json -e PRD_FILE=/Users/james/bookmarks-pdd-version/PRD.md -e APP_NAME=bookmarks-pdd-version --output /Users/james/bookmarks-pdd-version/prompts/api/staleness_review_Python.prompt
```


stdout:
```
Checking for updates...
Using .pddrc context: default
Input files:
  prompt_file     
/Users/james/miniconda/envs/pdd-vscode-extension/lib/python3.12/site-packages/pd
d/templates/generic/generate_prompt.prompt
Output files:
  output          
/Users/james/bookmarks-pdd-version/prompts/api/staleness_review_Python.prompt
Detected language: prompt
Basename: generate
╭──────────────────────────────────────────────────────────────────────────────╮
│ Starting prompt preprocessing                                                │
╰──────────────────────────────────────────────────────────────────────────────╯
Processing XML include: ./${PRD_FILE}
Warning: File not found: ${PRD_FILE}
Processing XML include: ./${API_DOC_FILE}
Warning: File not found: ${API_DOC_FILE}
Processing XML include: ./${DB_SCHEMA_FILE}
Warning: File not found: ${DB_SCHEMA_FILE}
Processing XML include: ./${BACKEND_FILES_CSV}
Warning: File not found: ${BACKEND_FILES_CSV}
Processing XML include: ./${IO_DEPENDENCIES_CSV}
Warning: File not found: ${IO_DEPENDENCIES_CSV}
Processing XML include: ./${ARCHITECTURE_FILE}
Warning: File not found: ${ARCHITECTURE_FILE}
Processing XML include: ./${TECH_STACK_FILE}
Warning: File not found: ${TECH_STACK_FILE}
Processing XML include: ./${CODE_GENERATOR_PROMPT}
Warning: File not found: ${CODE_GENERATOR_PROMPT}
Processing XML include: ./${PDDRC_FILE}
Warning: File not found: ${PDDRC_FILE}
╭──────────────────────────────────────────────────────────────────────────────╮
│ Preprocessing complete                                                       │
╰──────────────────────────────────────────────────────────────────────────────╯
╭──────────────────────────────────────────────────────────────────────────────╮
│ Starting prompt preprocessing                                                │
╰──────────────────────────────────────────────────────────────────────────────╯
Processing XML include: /Users/james/bookmarks-pdd-version/PRD.md
Processing XML include: ./${API_DOC_FILE}
Warning: File not found: ${API_DOC_FILE}
Processing XML include: ./${DB_SCHEMA_FILE}
Warning: File not found: ${DB_SCHEMA_FILE}
Processing XML include: ./${BACKEND_FILES_CSV}
Warning: File not found: ${BACKEND_FILES_CSV}
Processing XML include: ./${IO_DEPENDENCIES_CSV}
Warning: File not found: ${IO_DEPENDENCIES_CSV}
Processing XML include: ./architecture.json
Processing XML include: ./${TECH_STACK_FILE}
Warning: File not found: ${TECH_STACK_FILE}
Processing XML include: ./${CODE_GENERATOR_PROMPT}
Warning: File not found: ${CODE_GENERATOR_PROMPT}
Processing XML include: ./.pddrc
Warning: File not found: .pddrc
Including (many): ./${EXISTING_PROMPTS}
Warning: File not found: ${EXISTING_PROMPTS}
Doubling curly brackets...
╭──────────────────────────────────────────────────────────────────────────────╮
│ Preprocessing complete                                                       │
╰──────────────────────────────────────────────────────────────────────────────╯
Successfully loaded prompt: unfinished_prompt_LLM
Generated code saved to: 
/Users/james/bookmarks-pdd-version/prompts/api/staleness_review_Python.prompt

--- Command Execution Summary ---
  Step 1 (generate): Cost: $0.315920, Model: simple_extraction
Total Estimated Cost: $0.315920
-------------------------------------
📦 Debug snapshot saved to 
/Users/james/bookmarks-pdd-version/.pdd/core_dumps/pdd-core-20260313T221336Z.jso
n (attach when reporting bugs)
```

stderr:
```
2026-03-13 15:12:09,646 - pdd.llm_invoke - INFO - Loaded model data from package default
INFO: Loaded model data from package default
2026-03-13 15:12:09,655 - pdd.llm_invoke - WARNING - Multi-credential provider for model 'anthropic.claude-opus-4-6-v1' is missing env vars: AWS_ACCESS_KEY_ID, AWS_SECRET_ACCESS_KEY, AWS_REGION_NAME. Run 'pdd setup' to configure.
WARNING: Multi-credential provider for model 'anthropic.claude-opus-4-6-v1' is missing env vars: AWS_ACCESS_KEY_ID, AWS_SECRET_ACCESS_KEY, AWS_REGION_NAME. Run 'pdd setup' to configure.
2026-03-13 15:12:09,655 - pdd.llm_invoke - WARNING - Skipping GitHub Copilot model 'github_copilot/claude-opus-4.6-fast' in --force mode: no OAuth token found at /Users/james/.config/litellm/github_copilot/api-key.json. Run 'pdd setup' to authenticate.
WARNING: Skipping GitHub Copilot model 'github_copilot/claude-opus-4.6-fast' in --force mode: no OAuth token found at /Users/james/.config/litellm/github_copilot/api-key.json. Run 'pdd setup' to authenticate.
2026-03-13 15:12:09,655 - pdd.llm_invoke - WARNING - API key environment variable 'VERCEL_AI_GATEWAY_API_KEY' for model 'vercel_ai_gateway/anthropic/claude-opus-4.6' is not set.
WARNING: API key environment variable 'VERCEL_AI_GATEWAY_API_KEY' for model 'vercel_ai_gateway/anthropic/claude-opus-4.6' is not set.
2026-03-13 15:12:09,655 - pdd.llm_invoke - ERROR - API key 'VERCEL_AI_GATEWAY_API_KEY' not set. In --force mode, skipping interactive prompt.
ERROR: API key 'VERCEL_AI_GATEWAY_API_KEY' not set. In --force mode, skipping interactive prompt.
2026-03-13 15:12:09,655 - pdd.llm_invoke - WARNING - Multi-credential provider for model 'vertex_ai/claude-opus-4-6' is missing env vars: GOOGLE_APPLICATION_CREDENTIALS, VERTEXAI_PROJECT, VERTEXAI_LOCATION. Run 'pdd setup' to configure.
WARNING: Multi-credential provider for model 'vertex_ai/claude-opus-4-6' is missing env vars: GOOGLE_APPLICATION_CREDENTIALS, VERTEXAI_PROJECT, VERTEXAI_LOCATION. Run 'pdd setup' to configure.
[92m15:12:09 - LiteLLM:INFO[0m: utils.py:3932 - 
LiteLLM completion() model= claude-opus-4-6; provider = anthropic
INFO: 
LiteLLM completion() model= claude-opus-4-6; provider = anthropic
[92m15:13:31 - LiteLLM:INFO[0m: utils.py:1656 - Wrapper: Completed Call, calling success_handler
INFO: Wrapper: Completed Call, calling success_handler
2026-03-13 15:13:31,424 - pdd.llm_invoke - INFO - Loaded model data from package default
INFO: Loaded model data from package default
2026-03-13 15:13:31,514 - pdd.llm_invoke - WARNING - Multi-credential provider for model 'anthropic.claude-opus-4-6-v1' is missing env vars: AWS_ACCESS_KEY_ID, AWS_SECRET_ACCESS_KEY, AWS_REGION_NAME. Run 'pdd setup' to configure.
WARNING: Multi-credential provider for model 'anthropic.claude-opus-4-6-v1' is missing env vars: AWS_ACCESS_KEY_ID, AWS_SECRET_ACCESS_KEY, AWS_REGION_NAME. Run 'pdd setup' to configure.
2026-03-13 15:13:31,514 - pdd.llm_invoke - WARNING - Skipping GitHub Copilot model 'github_copilot/claude-opus-4.6-fast' in --force mode: no OAuth token found at /Users/james/.config/litellm/github_copilot/api-key.json. Run 'pdd setup' to authenticate.
WARNING: Skipping GitHub Copilot model 'github_copilot/claude-opus-4.6-fast' in --force mode: no OAuth token found at /Users/james/.config/litellm/github_copilot/api-key.json. Run 'pdd setup' to authenticate.
2026-03-13 15:13:31,514 - pdd.llm_invoke - WARNING - API key environment variable 'VERCEL_AI_GATEWAY_API_KEY' for model 'vercel_ai_gateway/anthropic/claude-opus-4.6' is not set.
WARNING: API key environment variable 'VERCEL_AI_GATEWAY_API_KEY' for model 'vercel_ai_gateway/anthropic/claude-opus-4.6' is not set.
2026-03-13 15:13:31,514 - pdd.llm_invoke - ERROR - API key 'VERCEL_AI_GATEWAY_API_KEY' not set. In --force mode, skipping interactive prompt.
ERROR: API key 'VERCEL_AI_GATEWAY_API_KEY' not set. In --force mode, skipping interactive prompt.
2026-03-13 15:13:31,514 - pdd.llm_invoke - WARNING - Multi-credential provider for model 'vertex_ai/claude-opus-4-6' is missing env vars: GOOGLE_APPLICATION_CREDENTIALS, VERTEXAI_PROJECT, VERTEXAI_LOCATION. Run 'pdd setup' to configure.
WARNING: Multi-credential provider for model 'vertex_ai/claude-opus-4-6' is missing env vars: GOOGLE_APPLICATION_CREDENTIALS, VERTEXAI_PROJECT, VERTEXAI_LOCATION. Run 'pdd setup' to configure.
[92m15:13:31 - LiteLLM:INFO[0m: utils.py:3932 - 
LiteLLM completion() model= claude-opus-4-6; provider = anthropic
INFO: 
LiteLLM completion() model= claude-opus-4-6; provider = anthropic
[92m15:13:36 - LiteLLM:INFO[0m: utils.py:1656 - Wrapper: Completed Call, calling success_handler
INFO: Wrapper: Completed Call, calling success_handler
```

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cli: prompt generation creates code file includes instead of example file includes #687

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