Extend configuration system to MCPs, agents, skills and more

[akbad]

Summary

This PR's main purpose is to migrate Bureau from shell-script-driven configuration into a YAML-driven, catalog-resolved system with declarative validation, dynamic skill installation and agent role management, and per-CLI setup plan rendering.

Main changes

• Added first set of Bureau-provided skills (6 editing modes + guided review mode), of which 2 are set up by Bureau by default

  • Included scripting for automatic installation/removal of these skills for all Bureau-supported coding agents

• Added full support for fully & concretely specifying MCPs, skills and agent role prompts in YML configs for maximal DRYness and user customizability

  • Implemented and documented full config schema for specifying MCPs' required settings & deps
  • Added scripted automation for setting up config-specified MCPs for all Bureau-configured coding agents
  • Removed hard-coded MCP choices and functionality idiosyncrasies from set-up-tools.sh (big boost to DRYness and maintainability)

• Added coding standards (in code-standards.md) as the 3rd must-read file for Bureau-configured agents (upon startup), containing high-quality coding guidelines distilled from my own work

  • However, code-standards.md is simply a default: users can configure what files agents read for this step to be custom style/standards files of their own (using the new code_standards setting)
  • These code standards are also integrated as part of the "quality check" phase in the newly-added assess mode skill

Extra changes included

Standardized logging

Refactored scripting to use these improved/preferred logging methods:

• Bash scripts now use Bureau's new internal Bash logging library at bin/lib/logging.sh
• Python scripts now use the Logger class

Trimmed redundant docs

The following documentation/Markdown files were removed due to simply being extra work to maintain while providing no tangible benefit:

• Supplementary detailed guides for agents on available MCP tools, both per-category and per-MCP (these were never needed by agents in practice)
• READMEs and extra legacy docs in tools/ and agents/

Other docs changed include:

• The subagent delegation/handoff guide (handoff-guide.md) was heavily trimmed and consolidated for conciseness and ease of navigation/reading

Fix obsolete paths in agent role prompts

• Paths in claude-subagents/ and role-prompts/ agent role definition files were updated to point to the appropriate files in protocols/context/static/

Miscellaneous

• Renamed check-prereqs script to ensure-prereqs for clarity
• Changed Qdrant MCP to now run statelessly (i.e. no session IDs needed), preventing all related errors that occurred sporadically when its tools were called by agents
• Updated obra/superpowers installer script for Codex and AGENTS.template.md to remove stale refs to the obsolete bootstrap script and instead use symlink-based install as prescribed by the upstream