* fix(agents): stop apply_patch from silently overwriting existing files
An "*** Add File:" hunk wrote its target unconditionally. When the path
already existed, apply_patch replaced the entire file, returned Success,
and listed the path under "added", so neither the model nor the UI got
any signal that existing content had been destroyed. The "*** Move to:"
destination of an update hunk had the same gap and reported the clobbered
path as merely modified.
The add and move-to branches now check the destination through the patch
file ops before writing and fail closed when it exists. Routing the check
through fileOps keeps it correct on all three backends (workspace-scoped
fs-safe root, raw fs, sandbox bridge). The check runs per hunk in patch
order, so deleting a path earlier in the same patch and recreating it
still works.
* fix(agents): make apply_patch destination creation atomic
The previous guard checked that an add or move-to destination was absent
and then wrote it. A competing writer could create the path in that gap,
after which the write still replaced it, so the no-clobber guarantee did
not hold under contention.
Destination creation now goes through a single exclusive create-if-absent
operation on every patch backend: Root.create for the workspace-scoped
default, an O_EXCL write for the raw filesystem, and a new pinned create
operation in the sandbox mutation helper that opens the target with
O_CREAT|O_EXCL and reports a reserved exit code when it already exists.
PatchFileOps drops its separate existence check.
Resolving the host ops behind an early return removes the repeated
workspaceOnly branch inside each operation and the optional-call dance
that let a missing root silently skip a write.
* fix(agents): complete atomic apply-patch creation
* fix(agents): preserve raced create replacements
* fix(agents): handle fs-safe patch collisions
* fix(agents): publish sandbox creates atomically
* test(agents): cover exclusive create provenance rollback
* fix(agents): use typed exclusive-create signal
---------
Co-authored-by: Vincent Koc <vincentkoc@ieee.org>
docs/concepts/context.md: replaced 12 curly quote and italic-marker
typography characters with ASCII equivalents so grep, copy-paste, and
Mintlify search hit clean tokens. Converted the 4-bullet Related list
into a CardGroup linking context-engine, compaction, system-prompt,
and agent-loop. Verified all four targets exist.
docs/concepts/soul.md: replaced 7 typography characters (curly
apostrophe in 'agent's' and similar) with ASCII equivalents. Renamed
'## Related docs' to '## Related' for consistency with sibling pages
and converted the 3-bullet list into a CardGroup linking
agent-workspace, system-prompt, and the SOUL.md template.
docs/tools/perplexity-search.md: removed the duplicate
'# Perplexity Search API' H1 (Mintlify renders title from frontmatter).
Replaced 2 typography characters and converted the 4-bullet Related
list into a CardGroup; verified web/brave-search/exa-search targets.
docs/tools/apply-patch.md: converted the 3-bullet Related list into a
CardGroup linking diffs, exec, and code-execution.
