feat: add 'todofinish' tool to mark tasks as completed in the todo list; update system prompts for task execution

src-misc/system-tools.txt

@@ -10,7 +10,7 @@ Core tools:
 - grep(pattern, path?) — Search for a pattern in files.
 - glob(pattern) — List files matching a glob pattern.
 - write(path, content, reason) — Write content to a file. Reason is required.
-- edit(path, old, new, reason) — Replace text in a file. Reason is required.
+- edit(path, old, new, replace_all?, reason) — Replace text in a file. Reason is required.
 - delete(path) — Delete a file or empty directory.
 - bash(command) — Run a shell command. Use for builds, tests, git ops.
 - bash_output(job_id) — Poll output of a background bash job.
@@ -18,6 +18,7 @@ Core tools:
 - cd(path) — Change working directory.
 - dir_list(path) — List directory contents.
 - dir_cache_update() — Refresh the directory cache.
+- pong(message?) — Simple connectivity check. Echoes back the message.
 
 Git tools:
 - git_operator(args, confirm_destructive?) — Run git commands. Some destructive
@@ -27,17 +28,20 @@ Git tools:
 
 
 Memory & Planning:
-- remember(text, type?) — Save to memory (type: lesson | reference | feedback).
-- recall(query) — Search memory for relevant entries.
+- remember(name, description, content, kind) — Save to memory (kind: project | reference | lesson | feedback).
+- recall(name?) — Read a specific memory entry, or list all if name is omitted.
 - forget(name) — Remove a memory entry.
-- plan_enter() — Enter plan mode (for planning before changes).
-- plan_ready() — Mark plan as ready for execution.
+- plan_enter(plan, sign_off) — Enter plan mode (provide a step-by-step plan and sign-off message).
+- plan_ready(confirmation) — Signal that you are ready to execute the approved plan.
 - seqthink(thought) — Record a chain-of-thought step.
+- todowrite(task) — Append a task to the session todo list.
+- todofinish(task_index?) — Mark a task (or all if omitted) as finished in todo.md.
 
 Workflow:
 - workflow_run(script, args) — Fan out work to sub-agents. Use for complex
   multi-step tasks needing parallel analysis or verification. Pass inline
   scripts with agent(), parallel(), and pipeline() primitives.
+- note_finding(text) — Share a finding with sibling agents in the same workflow run.
 
 Language Server Protocol (LSP) tools:
 - lsp_connect(name, command, args?, language_id) — Start an LSP server for a