docs: document global CLI flags and confirm noop.rs in architecture tree

[Copilot]

Weekly doc freshness audit flagged two drift issues in .github/copilot-instructions.md: noop.rs absent from the architecture tree listing, and the global --verbose/--debug flags missing from the CLI Commands section.

Changes

• Architecture tree — noop.rs was already present in the tree; no change required.
• CLI Commands — Added a global flags note at the top of the section documenting -v/--verbose (info-level logging) and -d/--debug (debug-level logging, implies verbose), which are defined as global = true on the Args struct in main.rs and apply to every subcommand.

### CLI Commands

Global flags (apply to all subcommands): `--verbose, -v` (enable info-level logging), `--debug, -d` (enable debug-level logging, implies verbose)

- `create` - Interactively create a new agent markdown file
  ...

Original prompt

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This section details on the original issue you should resolve

<issue_title>📝 Documentation drift detected — missing noop.rs in architecture tree and undocumented global CLI flags</issue_title>
<issue_description>## Documentation Freshness Audit

The weekly documentation audit found the following inconsistencies between code and documentation:

Findings

Area	Issue	File(s)
Architecture Section	tools/noop.rs is absent from the directory tree listing	.github/copilot-instructions.md
CLI Commands	--verbose / --debug global flags exist in the binary but are not documented	.github/copilot-instructions.md, agentic-pipelines/src/main.rs

Details

1. tools/noop.rs missing from architecture tree

The architecture tree under the Architecture section lists the tools/ directory as:

└── tools/            # MCP tool implementations
    ├── mod.rs
    ├── create_pr.rs
    ├── create_work_item.rs
    ├── memory.rs
    ├── missing_data.rs
    ├── missing_tool.rs
    └── result.rs

However, the actual agentic-pipelines/src/tools/ directory also contains noop.rs, which is a fully implemented tool (exported via mod.rs as pub use noop::*;). The noop tool itself is correctly documented in the Safe Output Tools section — only the file is missing from the architecture tree.

2. Global --verbose and --debug CLI flags are undocumented

agentic-pipelines/src/main.rs defines two global flags on the Args struct:

/// Enable verbose logging (info level)
#[arg(short, long, global = true)]
verbose: bool,
/// Enable debug logging (debug level, implies verbose)
#[arg(short, long, global = true)]
debug: bool,

These flags (-v/--verbose and -d/--debug) apply to every subcommand but are not mentioned anywhere in the CLI Commands section of the documentation.

Suggested Fixes

• Add noop.rs to the tools/ directory listing in the architecture tree
• Add a note about global flags (--verbose/--debug) in the CLI Commands section, e.g.:

  Global flags (apply to all subcommands): --verbose, -v (info logging), --debug, -d (debug logging, implies verbose)

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This issue was created by the automated documentation freshness check.

Generated by Documentation Freshness Check · ◷

Comments on the Issue (you are @copilot in this section)

• Fixes 📝 Documentation drift detected — missing noop.rs in architecture tree and undocumented global CLI flags #4

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