This part continues your part-one agent. Same repository, same command,
same model protocol — what grows is the set of tools behind it.

agent: started as: -C

The model reads a file through you. read takes a path (relative to
the working directory unless absolute) and returns the file's text as it
is — no banner, no line numbers, nothing added. Optional offset (the
1-based first line) and limit (how many lines) return a slice.

A path that does not exist is an error result, is_error: true, with a
content that says so. The loop goes on.

write takes a path and a content and puts exactly those bytes on
disk, creating parent directories on the way. The result is a short
confirmation; the file is the evidence.

An existing file is replaced whole. The content is written as given —
no trailing newline added, none removed.

edit replaces old_string with new_string in the file at path —
an exact, literal match, once. If old_string is not in the file, or is
in it more than once, nothing is written and the result is an error that
says which of the two it was. The model then knows to read more context
or give a longer anchor.

The rest of the file is untouched, byte for byte.

glob finds files by pattern, optionally under path. The result is
the matching paths, relative to the working directory, one per line,
sorted. * stays inside one path segment; ** crosses directories and
also matches none, so **/*.md finds a Markdown file at the top level
as well as three levels down.

grep searches file contents for a regular expression pattern, under
path (default: the working directory), optionally only in files whose
name matches glob. Every match is one line of the result:
path:line:text — the path relative to the working directory, the
1-based line number, the line as it is in the file.

A command that never returns must not take the agent with it. bash
accepts an optional timeout_ms (default 120000); a command still
running when it expires is killed, and its result is an error whose
content says timed out — along with whatever the command had printed
by then.

The whole thing takes about as long as the timeout, not as long as the
command wanted.

Without --yes, a tool call is checked before it runs:

.agent/settings.json
{"permissions": {"allow": ["bash(echo *)"], "deny": ["bash(rm *)"]}}

A rule names a tool (write) or a tool with a glob in parentheses —
matched against the command for bash, against the path for read,
write and edit. deny beats allow, allow beats the defaults,
and the defaults let read, glob and grep run while bash, write
and edit wait for a rule. A call that is not permitted does not run;
its result is is_error: true with a content starting permission denied. --yes allows everything that is not explicitly denied.

One reply may carry several tool_use blocks. Every one of them runs,
and the next request carries one user message with one tool_result
per call, in the order the calls were made — t1, t2, t3 — each
linked by its id. Whether they run at the same time or one after another
is your call; that all of them run and answer in order is not.

Every request also advertises all six tools by name.