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chore: Release version 0.6.0
Shell integration, Obsidian embeds, automatic dependency execution, and multi-argument CLI options. Release preparation includes: - Documentation fixes and reorganization - Test consolidation with shared helpers - DRY refactoring (shared option parsing) - Shell subcommand test coverage - Dead code cleanup 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
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‎CHANGELOG.md‎

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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
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and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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## [0.6.0] - 2025-11-29
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### Added
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- Shell integration with `wfw shell` subcommand: install, doctor, uninstall (32759ba, c0a49d6)
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- PS1 prompt integration via `__wfw_ps1()` function (1801cd7)
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- Obsidian markdown embed preprocessing: `![[file]]` syntax support (d3d1ccb)
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- Automatic dependency execution with execution caching (a51eeb1)
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- Multi-argument support for `--input`/`-in` and `--context`/`-cx` options (ee9e146)
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- Shell integration commands in installation guide (25dfa1a)
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- Pipeline module for dependency resolution and execution caching (a51eeb1)
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### Changed
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- Consolidated CONTEXT/INPUT config into single arrays for cleaner handling (e179184)
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- Reorganized reference and developer-guide documentation (ec75d6d, 8cab58f)
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- Updated user-guide for accuracy and formatting (c769c3c)
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- Documentation list separators enforced for mkdocs compatibility (e0702f6, e6031d7, f12aebc)
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- Pipeline and syntax documentation updates (b5d35ae)
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### Fixed
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- XML completion for builtin task templates (7d6950e)
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- Added doctor and uninstall to shell completions (e072ef6)
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## [0.5.0] - 2025-11-28
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### Added

‎CLAUDE.md‎

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## Version Management
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**Current version:** 0.5.0 (pre-release)
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**Current version:** 0.6.0 (pre-release)
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**Location:** `WIREFLOW_VERSION` in `wireflow.sh` (line 14)
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‎README.md‎

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**Reproducible AI Workflows for Research & Development**
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Version 0.5.0 (pre-release) · [Documentation](https://docs.joemona.co/wireflow/) · [GitHub](https://github.com/jdmonaco/wireflow)
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Version 0.6.0 (pre-release) · [Documentation](https://docs.joemona.co/wireflow/) · [GitHub](https://github.com/jdmonaco/wireflow)
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## Key Features
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‎RELEASE-NOTES.md‎

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# Release Notes
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## Version 0.6.0 (2025-11-29)
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**Shell Integration, Obsidian Embeds & Automatic Dependencies**
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This release adds seamless shell integration for prompt customization, Obsidian markdown embed support, and intelligent workflow caching with automatic dependency execution.
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### 🐚 Shell Integration
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Install WireFlow into your shell environment with a single command:
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```bash
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wfw shell install # Install wfw command, completions, and prompt helper
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wfw shell doctor # Check installation status and fix issues
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wfw shell uninstall # Remove shell integration
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```
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Customize your PS1 prompt with workflow-aware status:
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```bash
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source ~/.local/share/wireflow/wfw-prompt.sh
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PS1='$(__wfw_ps1) \$ ' # Shows current workflow context
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```
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### 📎 Obsidian Embed Support
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Use Obsidian's `![[file]]` syntax directly in task files:
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- `![[document.pdf]]` - Embeds PDF as content block
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- `![[image.png]]` - Embeds image via Vision API
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- `![[notes.md]]` - Inlines markdown content
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- Recursive embed resolution with cycle detection
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Perfect for researchers using Obsidian as a knowledge base.
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### 🔗 Automatic Dependency Execution
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Workflows with `DEPENDS_ON` now auto-execute stale dependencies:
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```bash
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wfw run analysis # Automatically runs prerequisite workflows first
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```
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Features:
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- Execution caching with hash-based staleness detection
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- Config/context/task changes trigger re-execution
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- Topological ordering ensures correct execution sequence
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### 📥 Multi-Argument Options
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Simplified file specification with multiple arguments per option:
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```bash
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# Multiple inputs in one flag
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wfw run analysis -in file1.txt file2.txt file3.txt
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# Multiple context files
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wfw run summary -cx ref1.pdf ref2.pdf
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# Mix with other options
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wfw run report -in data.csv -cx guide.md --profile deep
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```
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---
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## Version 0.5.0 (2025-11-28)
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**Batch Processing, Model Profiles & Image Format Conversion**

‎docs/developer-guide/architecture.md‎

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├── core.sh # Subcommand implementations (init, new, edit, list, config)
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├── config.sh # Configuration loading and cascade logic
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├── help.sh # Help text for all subcommands
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├── pipeline.sh # Dependency resolution and execution caching
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├── run.sh # Run mode (workflow execution with full context)
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├── task.sh # Task mode (lightweight execution without workflow dirs)
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├── batch.sh # Batch mode (Message Batches API)

‎docs/developer-guide/implementation.md‎

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- Git-style format: usage line, options, description, examples
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- Sourced early, integrated via `help` subcommand and `-h` flags
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### lib/pipeline.sh
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**Dependency resolution and execution caching:**
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- `write_execution_log()` - Write execution.json after successful workflow completion
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- `read_execution_log()` - Parse execution log for staleness checks
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- `compute_execution_hash()` - Generate 16-character hash of execution state
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- `is_execution_stale()` - Check if workflow needs re-run (mtime + hash validation)
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- `get_staleness_reason()` - Return human-readable reason for staleness
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- `extract_depends_on()` - Parse DEPENDS_ON from workflow config
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- `resolve_dependency_order()` - Topological sort for dependency chain
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- `execute_dependency()` - Run dependency workflow in isolated subprocess
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- `reset_workflow_config()` - Restore project-level config from cache
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- `get_execution_status()` - Format status for workflow listing
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- `get_execution_timestamp()` - Format last execution time
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**Key concepts:**
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- Execution hash combines: config state, file hashes, dependency hashes, task file hash
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- Fast path uses mtime checks, slow path uses full hash comparison
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- Subshell isolation prevents dependency config from polluting parent
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### lib/task.sh
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**Task mode execution:**

‎docs/index.md‎

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**Reproducible AI Workflows for Research & Development**
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Version 0.5.0 (pre-release)
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Version 0.6.0 (pre-release)
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## Key Features
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‎docs/user-guide/configuration.md‎

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| Variable | Description | Default |
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|----------|-------------|---------|
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| `OUTPUT_FORMAT` | File extension (`md`, `txt`, `json`) | `md` |
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| `EXPORT_FILE` | Additional output path | (empty) |
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| `EXPORT_PATH` | Additional output path | (empty) |
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| `SYSTEM_PROMPTS` | Prompt names | `(base)` |
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| `WIREFLOW_PROMPT_PREFIX` | Prompts directory | `~/.config/wireflow/prompts` |
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| `-in/--input` | `INPUT` | `-in data.csv` |
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| `-cx/--context` | `CONTEXT` | `-cx notes.md` |
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| `--depends-on` | `DEPENDS_ON` | `--depends-on preprocessing` |
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| `--export-file` | `EXPORT_FILE` | `--export-file reports/out.md` |
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| `--export` | `EXPORT_PATH` | `--export reports/out.md` |
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## Viewing Configuration
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‎lib/config.sh‎

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</user-task>
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TASK_EOF
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#TODO fix builtin task templates with incomplete XML structure
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# summarize.txt
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cat > "$task_dir/summarize.txt" <<'TASK_EOF'
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<user-task>

‎lib/execute.sh‎

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# This file is sourced by wireflow.sh and lib/task.sh.
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# =============================================================================
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# =============================================================================
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# Shared Option Parsing
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# =============================================================================
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# Parse common execution options shared between run and task modes
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# Arguments:
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# $1 - option: The option flag being parsed
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# $2+ - remaining arguments
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# Returns:
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# Sets PARSE_CONSUMED to number of args consumed (0 = unknown option)
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# Sets global config variables (MODEL, TEMPERATURE, etc.)
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# Usage:
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# parse_common_option "$1" "${@:2}"
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# if [[ $PARSE_CONSUMED -gt 0 ]]; then
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# shift $PARSE_CONSUMED
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# fi
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PARSE_CONSUMED=0
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parse_common_option() {
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local opt="$1"
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shift
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PARSE_CONSUMED=0
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case "$opt" in
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--profile)
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[[ $# -eq 0 ]] && { echo "Error: --profile requires argument" >&2; return 1; }
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PROFILE="$1"
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CONFIG_SOURCE_MAP[PROFILE]="cli"
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PARSE_CONSUMED=2
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;;
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--model|-m)
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[[ $# -eq 0 ]] && { echo "Error: --model requires argument" >&2; return 1; }
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MODEL="$1"
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CONFIG_SOURCE_MAP[MODEL]="cli"
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PARSE_CONSUMED=2
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;;
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--enable-thinking)
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ENABLE_THINKING=true
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CONFIG_SOURCE_MAP[ENABLE_THINKING]="cli"
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PARSE_CONSUMED=1
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;;
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--disable-thinking)
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ENABLE_THINKING=false
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CONFIG_SOURCE_MAP[ENABLE_THINKING]="cli"
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PARSE_CONSUMED=1
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;;
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--thinking-budget)
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[[ $# -eq 0 ]] && { echo "Error: --thinking-budget requires argument" >&2; return 1; }
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THINKING_BUDGET="$1"
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CONFIG_SOURCE_MAP[THINKING_BUDGET]="cli"
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PARSE_CONSUMED=2
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;;
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--effort)
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[[ $# -eq 0 ]] && { echo "Error: --effort requires argument" >&2; return 1; }
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EFFORT="$1"
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CONFIG_SOURCE_MAP[EFFORT]="cli"
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PARSE_CONSUMED=2
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;;
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--temperature|-t)
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[[ $# -eq 0 ]] && { echo "Error: --temperature requires argument" >&2; return 1; }
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TEMPERATURE="$1"
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CONFIG_SOURCE_MAP[TEMPERATURE]="cli"
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PARSE_CONSUMED=2
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;;
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--max-tokens)
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[[ $# -eq 0 ]] && { echo "Error: --max-tokens requires argument" >&2; return 1; }
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MAX_TOKENS="$1"
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CONFIG_SOURCE_MAP[MAX_TOKENS]="cli"
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PARSE_CONSUMED=2
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;;
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--system|-p)
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[[ $# -eq 0 ]] && { echo "Error: --system requires argument" >&2; return 1; }
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IFS=',' read -ra SYSTEM_PROMPTS <<< "$1"
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CONFIG_SOURCE_MAP[SYSTEM_PROMPTS]="cli"
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PARSE_CONSUMED=2
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;;
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--format|-f)
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[[ $# -eq 0 ]] && { echo "Error: --format requires argument" >&2; return 1; }
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OUTPUT_FORMAT="$1"
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CONFIG_SOURCE_MAP[OUTPUT_FORMAT]="cli"
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PARSE_CONSUMED=2
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;;
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--enable-citations)
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ENABLE_CITATIONS=true
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CONFIG_SOURCE_MAP[ENABLE_CITATIONS]="cli"
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PARSE_CONSUMED=1
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;;
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--disable-citations)
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ENABLE_CITATIONS=false
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CONFIG_SOURCE_MAP[ENABLE_CITATIONS]="cli"
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PARSE_CONSUMED=1
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;;
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*)
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# Unknown option - caller handles
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PARSE_CONSUMED=0
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;;
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esac
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return 0
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}
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# =============================================================================
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# System Prompt Building
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# =============================================================================

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