Add progress callback to run_one_agent and run_and_apply so callers
can see: prompt size, node list, LLM call timing, parsed action
count, and per-action applied/skipped status. Daemon writes these
to the persistent event log via log_event.
Cap organize cluster to 20 nodes - 126 nodes produced a 682KB
prompt that timed out every time. Agent has tools to explore
further if needed. Restore general query for production runs.
Previous prompt was too documentation-heavy — agent pattern-matched
on example placeholders instead of doing actual work. New prompt:
structured as direct instructions, uses {{organize}} placeholder
for pre-computed cluster data, three clear decision paths (merge,
differentiate, keep both), numbered rules.
Add `poc-memory graph organize TERM` diagnostic that finds nodes
matching a search term, computes pairwise cosine similarity, reports
connectivity gaps, and optionally creates anchor nodes.
Add organize.agent definition that uses Bash(poc-memory:*) tool access
to explore clusters autonomously — query selects highest-degree
unvisited nodes, agent drives its own iteration via poc-memory CLI.
Add {{organize}} placeholder in defs.rs for inline cluster resolution.
Add `tools` field to AgentDef/AgentHeader so agents can declare
allowed tool patterns (passed as --allowedTools to claude CLI).
