CI: apply-in-place - #43

Since yas-run#54 a command wait that runs out before any command it could
report on has started answers TIMEOUT (NOT_FOUND stays for an exited
terminal or an evicted index). The client_host test still expected
NOT_FOUND, so it failed on main.

Since yas-run#54 the server answers TIMEOUT when a command wait runs out before
any command it could report on has started; wait_terminal_command's
documentation still said NOT_FOUND, which stays for an evicted index or
an exited terminal.

APPLY WRITE_INLINE items take item flag APPLY_ITEM_IN_PLACE (2), offered
with CAPABILITY_APPLY_IN_PLACE (32): the item writes as COMMIT of a
STAGE_IN_PLACE stage does (open with create and truncate through a final
symlink, no temporary, no rename), through one shared write_in_place. An
in-place write onto a directory is CONFLICT with {EISDIR, open} in the
item's ApplyOsErrors entry, as COMMIT's. The flag is INVALID on other item
kinds and with APPLY_ITEM_CREATE_PARENTS; APPLY_ITEM_EXTENDED_FLAGS lists it
beside the v1 baseline's APPLY_ITEM_FLAGS.

yas-client's write_in_place sends it for content within the server's
inline limit and stages the rest, so a write tool call that already spends
a round trip resolving or reading the file takes two in all, not three.
TypeScript codec parity (inPlace) and golden vector
fs.apply.in_place.payload.

Review of yas-run#89: the mode an in-place write gives a file it creates is read
under cfg(unix) alone, so Windows' -D warnings build failed on dead_code
(Stage::mode had atomic_replace to read it). Windows files take their
directory's ACL; say so on the field. Rewrap yas.md's opt-in paragraph at 80
columns.