feat(plugin): add structured debug logging and skill progress reporting

[onlycastle]

Summary

• Add environment-gated debug logger (BETTERPROMPT_DEBUG=1) that writes to stderr, preserving JSON-RPC on stdout
• Instrument hooks, debounce state machine, config, native deps, and MCP server with structured debug/info/error calls
• Standardize [bp] progress status lines across all 14 analysis skills
• Enhance wrapToolExecution with tool-name tracking and duration metrics

Changes

1. feat(plugin): add structured debug logger utility — new lib/logger.ts
2. feat(plugin): instrument hooks and core libs with debug logging — hooks, config, debounce, native-deps
3. feat(plugin): instrument MCP server with debug logging — server.ts, server-entry.ts
4. feat(plugin): add progress reporting to analysis skills — 14 SKILL.md files
5. chore(plugin): rebuild dist

Test Plan

• TypeScript type-check passes (npx tsc --noEmit)
• All 452 tests pass (npm test)
• Build succeeds (npx tsup)
• Manual: set BETTERPROMPT_DEBUG=1 and verify stderr logging output
• Manual: run /bp-analyze and verify [bp] progress lines appear

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[onlycastle]

Code Review

Found 2 issues:

1. info() is gated identically to debug() — the 3-tier severity model is broken
   info and debug both no-op unless BETTERPROMPT_DEBUG=1, but info is used for operationally important events: server lifecycle (start/connected/shutdown), native dep installation, and bootstrap milestones. The logger establishes a debug < info < error hierarchy where only error is always-on, making the debug/info distinction meaningless. Consider making info always-on like error, or rename all info calls to debug to match actual behavior.
   https://github.com/onlycastle/BetterPrompt/blob/ec9b0ab/packages/plugin/lib/logger.ts#L25-L28

2. New file and pipeline changes not documented in docs/agent/
   CLAUDE.md requires: "When you add new files, change directory structure, modify the pipeline... update the relevant docs/agent/ doc in the same change." A new shared module lib/logger.ts was added and the plugin pipeline was instrumented with debug logging, but docs/agent/PLUGIN.md and docs/agent/ARCHITECTURE.md were not updated to document BETTERPROMPT_DEBUG or the logger module.
   https://github.com/onlycastle/BetterPrompt/blob/ec9b0ab/packages/plugin/lib/logger.ts#L1

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