Problem

Mode-specific rule files (e.g. .kilocoderules-code, .kilo/rules-code/*.md) are loaded into the generic instructions array alongside non-mode-specific rules. This means all mode-tagged rules are injected into the system prompt for every agent, regardless of which agent/mode is currently active.

For example, if a project has:

• .kilocoderules-code (rules for the code mode)
• .kilocoderules-architect (rules for the architect mode)
• .kilo/rules/general.md (generic rules)

All three files are included in the system prompt even when only the code agent is active. The architect-specific rules should not be present when running in code mode, and vice versa.

Additional issue: custom mode rules are never discovered

Custom modes defined in .kilocodemodes are not scanned for rule directories. The rule discovery logic uses a hardcoded KNOWN_MODES list (code, architect, ask, debug, orchestrator), so if a user defines a custom mode (e.g. translate) and creates a corresponding .kilo/rules-translate/ directory, those rules are silently ignored.

Expected behavior

1. Mode-specific rules should only be injected into the system prompt for the matching active agent/mode. Generic rules (non-mode-tagged) should continue to apply to all agents.
2. Custom modes defined in .kilocodemodes should have their rule directories discovered alongside the built-in modes, so that .kilo/rules-{custom-mode}/*.md and .kilocoderules-{custom-mode} files are properly loaded.

Steps to reproduce

1. Create a project with mode-specific rules for multiple modes:

   .kilocoderules-code    -> "# Code-only rules"
   .kilocoderules-architect -> "# Architect-only rules"
   

2. Start a session with the code agent
3. Inspect the system prompt — both code and architect rules are present

For the custom mode issue:

1. Define a custom mode translate in .kilocodemodes
2. Create .kilo/rules-translate/glossary.md
3. Start a session with the translate agent
4. The glossary rules are never loaded

Related PR

#7478