feat: Add option to disable backup file creation in agents and CLI

[FraserKillip]

Solves #61

[intellectronica]

@FraserKillip thanks for the contribution 🙏 Are you OK to fix the linting errors so that we can land this?

[intellectronica]

This

 if (!agentConfig?.disableBackup) {
    await backupFile(output);
 }

is now repeated so many times across all agents.

Surely we can find a way to implement this that only checks once.

[Copilot]

Pull Request Overview

Adds a --disable-backup CLI option to prevent creation of .bak backup files when applying agent configurations, addressing issue #61 by providing users control over backup file generation.

• Adds disableBackup parameter throughout the configuration chain from CLI to individual agents
• Updates all agent implementations to conditionally skip backup creation when flag is enabled
• Includes comprehensive test coverage for the new functionality across all agent types

Reviewed Changes

Copilot reviewed 17 out of 17 changed files in this pull request and generated 9 comments.

Show a summary per file

File	Description
src/cli/commands.ts	Adds the --disable-backup CLI option and passes it to the apply function
src/lib.ts	Propagates the disableBackup flag from CLI to agent configurations
src/agents/IAgent.ts	Extends the IAgentConfig interface to include the disableBackup option
src/agents/*.ts	Updates all agent implementations to conditionally skip backup creation
tests/unit/agents/AgentAdapters.test.ts	Adds comprehensive test coverage for backup disabling functionality
README.md	Documents the new --disable-backup CLI option with usage examples

[FraserKillip]

@FraserKillip thanks for the contribution 🙏 Are you OK to fix the linting errors so that we can land this?

@intellectronica 💯 will get this all tidied up. Might take me a couple days between priorities

[FraserKillip]

@intellectronica I think this should be ready for re-review when you have the time :ty: