CLI Reference confusing dry-run flag documentation for execute and run commands

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Drift detected

Source: src/cli.ts (execute command: lines 197-198, run command: lines 279-280)
Docs: docs/02-reference/01-cli.md (execute and run command sections)

What's wrong in docs

The documentation oversimplifies the dual flag system for dry-run behavior, making it confusing for users.

Current docs show:

• Only mentions --execute flag with description "Actually run (without this flag, dry-run)"

Source code shows:

• execute command has both .option("--dry-run", "Log actions without executing", true) and .option("--execute", "Actually execute the plan (opt-in)", false)
• run command has both .option("--dry-run", "Log actions without executing (default)", true) and .option("--execute", "Actually execute the plan (opt-in)", false)

Impact

Users don't understand that:

1. Both commands default to dry-run mode
2. There are two ways to control execution: --dry-run and --execute
3. The flags work as mutually exclusive options where --execute overrides the default --dry-run=true

This leads to confusion about which flag to use and the default behavior.

Suggested fix

Update the CLI reference to show both flags clearly for execute and run commands:

| `--dry-run` | `true` | Log actions without executing (default) |
| `--execute` | `false` | Actually execute the plan (opt-in) |

And clarify in the description that these commands default to dry-run mode for safety.

Related

Related to existing issues #9 and #2 about dry-run behavior confusion.