fix: comprehensive cli.md — all subcommands and flags

Major additions:
- thread: list/show/inspect/kill with all flags
- remote: add/list/show/set-url/set-token/remove/default
- init: --from, --force
- dev/start: --port
- daemon: restart subcommands
- sense/workflow: all flags
- logs: --offset
- store archive: --vacuum
- workspace layout: updated with workflow structure

.knowledge/cli.md

@@ -5,33 +5,54 @@
 ## Workspace Lifecycle
 
 ```bash
-nerve init                    # scaffold a new workspace (nerve.yaml, senses/, workflows/)
+nerve init                    # scaffold workspace (nerve.yaml, senses/, workflows/)
+nerve init --from <git-url>   # clone existing workspace from git
+nerve init --force            # reinitialize (preserves data/)
 nerve validate                # validate nerve.yaml config
 nerve dev                     # run kernel foreground (development, Ctrl+C to stop)
+nerve dev --port 3000         # with HTTP API on specific port
 nerve start                   # start daemon (background)
+nerve start --port 3000       # with HTTP API port
 nerve stop                    # stop daemon
 nerve status                  # check daemon health (uptime, senses, workflows)
-nerve daemon                  # restart daemon (stop + start)
+nerve daemon restart           # stop + start
+nerve daemon logs             # alias for nerve logs
 ```
 
 ## Sense Management
 
 ```bash
 nerve create sense <name>     # scaffold a new sense (compute.ts + schema.ts)
-nerve sense list              # list configured senses
+nerve create sense <name> --force  # overwrite existing
+nerve sense list              # list configured senses and status
 nerve sense trigger <name>    # manually trigger a sense compute
-nerve sense schema <name>     # show sense Drizzle schema
-nerve sense query <name>      # inspect sense SQLite database
-nerve sense query <name> --sql "SELECT * FROM samples LIMIT 5"
+nerve sense schema <name>     # print CREATE TABLE statements from sense SQLite
+nerve sense schema <name> --json   # as JSON array
+nerve sense query <name>      # inspect sense SQLite database (preview rows)
+nerve sense query <name> --json    # rows as JSON
 ```
 
 ## Workflow Management
 
 ```bash
 nerve create workflow <name>  # scaffold a new workflow
+nerve create workflow <name> --force  # overwrite existing
+nerve workflow list           # list workflow definitions from nerve.yaml
+nerve workflow status         # show live status (concurrency, active, queued)
 nerve workflow trigger <name> --prompt "..." [--max-rounds N] [--dry-run]
-nerve workflow list           # list configured workflows
-nerve thread                  # list active (queued/started) workflow threads
+```
+
+## Thread Management
+
+```bash
+nerve thread list             # list active (queued/started) workflow runs
+nerve thread list --all       # include completed/failed/crashed
+nerve thread list --workflow <name>  # filter by workflow name
+nerve thread show <runId>     # print role rounds for a run (agent-oriented)
+nerve thread show <runId> --before N  # limit rounds (pagination)
+nerve thread inspect <runId>  # show details and thread events
+nerve thread inspect <runId> --offset N --limit N  # paginate events
+nerve thread kill <runId>     # kill a running or queued thread
 ```
 
 ## Knowledge
@@ -41,21 +62,30 @@ nerve knowledge sync          # chunk files per knowledge.yaml, compute embeddin
 nerve knowledge query "text"  # search indexed knowledge (cosine similarity)
 nerve knowledge query -g "text"           # global search across all indexed repos
 nerve knowledge query --repo /path "text" # search specific repo
+nerve knowledge query "text" --limit 20   # max hits (default 10)
 ```
 
 ## Logs & Store
 
 ```bash
-nerve logs                    # view daemon logs (last 50 lines)
-nerve logs -f                 # follow logs (tail -f style)
+nerve logs                    # show daemon log output (last 50 lines)
 nerve logs -n 200             # last N lines
-nerve store archive           # archive old log entries to JSONL
+nerve logs --offset 100       # start from line N (pagination)
+nerve logs -f                 # follow logs (tail -f style)
+nerve store archive           # archive logs older than 30 days to JSONL
+nerve store archive --vacuum  # also run SQLite VACUUM after archiving
 ```
 
-## Remote
+## Remote Management
 
 ```bash
-nerve remote add <name> <url> # add a remote daemon endpoint
+nerve remote add <name> <host:port> [--token <token>]  # add remote daemon
+nerve remote list             # list all remotes
+nerve remote show <name>      # show remote details
+nerve remote set-url <name> <host:port>   # update remote host
+nerve remote set-token <name> <token>     # update remote token
+nerve remote remove <name>    # remove a remote
+nerve remote default [<name>] # set or show default remote
 nerve status --remote <name>  # check remote daemon health
 ```
 
@@ -67,12 +97,22 @@ my-agent/
   knowledge.yaml              # knowledge index config (optional)
   senses/
     cpu-usage/
-      compute.ts              # sense implementation
-      schema.ts               # Drizzle schema
-      migrations/             # auto-generated
+      src/
+        index.ts              # sense compute implementation
+        schema.ts             # Drizzle schema (single source of truth)
+      migrations/             # auto-generated by drizzle-kit
+      package.json            # with esbuild build script
+      index.js                # bundled output (generated by pnpm build)
   workflows/
     cleanup/
       src/index.ts            # workflow definition
+      build.ts                # factory function
+      moderator.ts            # moderator + meta types
+      roles/                  # one file per role
+      package.json
+  data/
+    senses/                   # per-sense SQLite databases
+    archive/                  # archived logs (JSONL)
   knowledge.db                # generated by nerve knowledge sync
   .knowledge/                 # curated knowledge cards
 ```