keboola · padak · Aug 25, 2026 · Aug 25, 2026 · Aug 25, 2026 · Aug 25, 2026
diff --git a/CLAUDE.md b/CLAUDE.md
@@ -838,6 +838,18 @@ kbagent sync pull --project ALIAS [--all-projects] [--force] [--theirs] [--dry-r
 kbagent sync status [--directory DIR]
 kbagent sync diff --project ALIAS [--all-projects] [--directory DIR] [--branch ID]
 kbagent sync push --project ALIAS [--all-projects] [--dry-run] [--force] [--allow-plaintext-on-encrypt-failure] [--branch ID] [--no-name-drift-warnings]
+# sync push (since vNEXT, #686): the manifest baseline `pull_config_hash` is stamped from the API
+#   response (or a read-back), never from disk -- push-deployed multi-statement SQL transformations
+#   (and anything disabled in the UI whose local YAML lacks `is_disabled`) no longer show permanent
+#   phantom `~ REMOTE MODIFIED` drift in `sync diff`. Unreadable-after-write leaves the baseline
+#   UNTOUCHED + a `warnings[]` entry (never a disk-derived fallback). One canonical script[] shape now
+#   (one element = one statement) and `transform.sql` gains `/* ===== STATEMENT ===== */` markers when
+#   semicolons cannot recover the boundaries -- which also closes a SILENT pre-vNEXT rewrite that
+#   collapsed such scripts to one statement (MULTI_STATEMENT_COUNT=1) while diff said "in sync".
+#   Migration: entries carry `metadata.config_hash_version`; unversioned ones match leniently (pre-vNEXT
+#   hash of the SAME remote counts as in sync, nothing else), and ONE `sync pull` per project migrates.
+#   A pre-markers tree whose only difference from the remote is the lost boundaries is REFUSED per-change
+#   with SYNC_LEGACY_BOUNDARY telling you to pull first; genuine edits push normally.
 # sync diff/push (0.89.0+, #649): local side read from exactly ONE tree (target branch subtree, else main/); entries tracked on another branch's tree are excluded from the changeset and reported under orphaned[] + summary.orphaned (reasons + reconcile hints); fix with sync pull. Adopt-by-id is branch-aware.
 # Ignored components (since vNEXT, #689): keboola.mcp-server-tool joins keboola.sandboxes on ALWAYS_IGNORED_COMPONENTS (the MCP server's auto-created empty mcp-workspace-<hex> configs); the manifest field ignoredComponents (.keboola/manifest.json) is now LIVE and unions with the hardcoded set, honored by pull/diff/push. pull drops manifest entries + local dirs for a newly-ignored component, reported with action "ignored" (distinct from "removed" = deleted on remote); diff filters the local side too, so a stale dir for an ignored component can never classify as DELETED -- closes the delete-dir-then-push trap that used to destroy production keboola.mcp-server-tool configs.
 kbagent sync clone --source DIR --target ALIAS --target-dir DIR [--bucket-map FILE] [--variable-values FILE] [--instance-rename FILE] [--dry-run] [--branch ID]

diff --git a/docs/error-codes.md b/docs/error-codes.md
@@ -130,6 +130,7 @@ of `ErrorCode` in `src/keboola_agent_cli/errors.py`.
 | `PARENT_CONFIG_NOT_TRACKED` | Row operation references a parent config not in the manifest |
 | `VARIABLE_LINK_UNRESOLVED` | `sync push` could not resolve a transformation's variables link to a tracked config |
 | `SYNC_CONFLICT` | `sync pull --force` aborted: local and remote both changed since the last pull (`details.conflicts` lists them) |
+| `SYNC_LEGACY_BOUNDARY` | `sync push` refused one config: the working tree predates statement-boundary tracking, so pushing it would merge separate SQL statements into one. Run `sync pull` first |
 
 ### Encryption
 

diff --git a/plugins/kbagent/agents/keboola-expert.md b/plugins/kbagent/agents/keboola-expert.md
@@ -257,7 +257,11 @@ its absence is NOT a promise the entry is version-independent (see §1 Rule 6).
   `never_fetched` warning on diff/push = run `sync pull` first; a non-zero
   `summary.orphaned` (0.89.0+, #649) = the manifest is targeted at another
   branch's tree -- `sync pull` to re-target, never push. `sync status`
-  is local-only -- audit real drift with `sync diff`.
+  is local-only -- audit real drift with `sync diff`. On <= 0.90.1 a
+  `~ REMOTE MODIFIED ... codes changed` on a config nobody touched is usually
+  PHANTOM (issue #686: push stamped the baseline from disk); fixed in vNEXT --
+  one `sync pull` per project migrates a tree pulled by an older version, and
+  a `SYNC_LEGACY_BOUNDARY` push error means exactly that: pull first.
 - **Ignored components** (vNEXT, #689): `keboola.sandboxes` +
   `keboola.mcp-server-tool` are always excluded from `pull`/`diff`/`push`,
   unioned with the manifest's `ignoredComponents` list. A component newly

diff --git a/plugins/kbagent/skills/kbagent/references/commands-reference.md b/plugins/kbagent/skills/kbagent/references/commands-reference.md
@@ -326,9 +326,9 @@ Requires the project to be added with its **master ('owner') Storage API token**
 ## Sync (GitOps)
 - `sync init --project ALIAS [--directory DIR] [--git-branching] [--adopt-existing]` -- initialize sync working directory; `--adopt-existing` (since v0.22.0) adopts a `.keboola/manifest.json` already written by the kbc Go CLI without overwriting (idempotent; validates `project_id` against the alias token)
 - `sync pull --project ALIAS [--all-projects] [--force] [--theirs] [--dry-run] [--with-samples] [--no-storage] [--no-jobs] [--job-limit N] [--branch ID]` -- download configs to local files. For large projects (>100 configs), automatically fetches jobs per-config when the grouped API limit is insufficient. `--force` is conflict-aware (since 0.53.0): a locally-modified config whose remote is unchanged is **preserved** (pending delta stays pushable, never silently re-stamped); a true merge conflict (local AND remote both changed since last pull) **aborts** the pull (exit 1, `SYNC_CONFLICT`; `--json` lists `details.conflicts`); local-untouched + remote-changed takes remote. `--theirs` (since v0.72.0) is the supported "discard local, take production" reconcile path: overwrites locally-modified configs/rows, restores deleted/missing files, resolves conflicts by taking remote (no abort, no manifest surgery). Since v0.72.0 plain pull also re-materializes a tracked config whose local dir was deleted (manifest<->disk invariant), so delete-dir-then-pull refetches. Config-level `isDisabled` round-trips (since v0.72.0) as sparse `is_disabled: true` in `_config.yml` -- absent key = enabled. `--branch` (0.47.0+) per-invocation dev-branch override, beats every other branch source. Ignored components (since vNEXT): `keboola.sandboxes` + `keboola.mcp-server-tool` are always excluded, unioned with the manifest's `ignoredComponents` list; a component newly ignored has its manifest entry dropped and local directory removed, reported with pull action `"ignored"` (distinct from `"removed"` = genuinely deleted on remote).
-- `sync push --project ALIAS [--all-projects] [--dry-run] [--force] [--allow-plaintext-on-encrypt-failure] [--branch ID] [--no-name-drift-warnings]` -- push local changes (auto-encrypts secrets, fails if encryption fails). Fresh-CREATE writeback updates placeholder manifest entries in place (since 0.47.0) and propagates any `KBC.configuration.*` metadata via `set_config_metadata`. Fresh-CREATE variable binding (since 0.47.2): when a `keboola.variables` config + its values row are created alongside a transformation in the same push, the transformation's `variables_id` / `variables_values_id` placeholders are rebound to the assigned ULIDs and the row's `values` are hoisted even without a `_keboola` block, so `job run` succeeds with no post-push `config variables-set` step (unresolvable/ambiguous links surface a `variable_link` entry in `errors[]`, never a broken link). Never-fetched guard (since v0.72.0): a manifest entry with an empty `pull_hash` and no local files (pre-0.72 name-collision phantom) is **never** planned as a remote DELETE -- diff/push exclude it and report it under `never_fetched` with a warning (run `sync pull` to materialize); local deletion of a properly-pulled config still deletes on push. Adopted-by-id writeback (since v0.72.0): pushing an untracked file whose `_keboola.config_id` resolves on the branch also writes the manifest entry, so follow-up diffs are stable. `--branch` (0.47.0+) per-invocation override; when no `<branch_name>/` subtree exists on disk (since 0.47.2) the local default tree (`main/`) is promoted to the target branch (API writes still target the branch id); `--no-name-drift-warnings` (0.47.0+) drops the cosmetic warnings array. Branch-scoped since v0.89.0 (issue #649): push consumes the diff's changeset, so configs tracked on another branch's tree are never planned as creates -- they ride along on the result envelope under `orphaned` instead (see `sync diff`). Ignored components (since vNEXT) are filtered out on both sides of the diff push builds on, so a stale local directory for an ignored component (e.g. `keboola.mcp-server-tool`) is never classified as `DELETED` and can never be pushed as a remote deletion.
+- `sync push --project ALIAS [--all-projects] [--dry-run] [--force] [--allow-plaintext-on-encrypt-failure] [--branch ID] [--no-name-drift-warnings]` -- push local changes (auto-encrypts secrets, fails if encryption fails). Fresh-CREATE writeback updates placeholder manifest entries in place (since 0.47.0) and propagates any `KBC.configuration.*` metadata via `set_config_metadata`. Fresh-CREATE variable binding (since 0.47.2): when a `keboola.variables` config + its values row are created alongside a transformation in the same push, the transformation's `variables_id` / `variables_values_id` placeholders are rebound to the assigned ULIDs and the row's `values` are hoisted even without a `_keboola` block, so `job run` succeeds with no post-push `config variables-set` step (unresolvable/ambiguous links surface a `variable_link` entry in `errors[]`, never a broken link). Never-fetched guard (since v0.72.0): a manifest entry with an empty `pull_hash` and no local files (pre-0.72 name-collision phantom) is **never** planned as a remote DELETE -- diff/push exclude it and report it under `never_fetched` with a warning (run `sync pull` to materialize); local deletion of a properly-pulled config still deletes on push. Adopted-by-id writeback (since v0.72.0): pushing an untracked file whose `_keboola.config_id` resolves on the branch also writes the manifest entry, so follow-up diffs are stable. `--branch` (0.47.0+) per-invocation override; when no `<branch_name>/` subtree exists on disk (since 0.47.2) the local default tree (`main/`) is promoted to the target branch (API writes still target the branch id); `--no-name-drift-warnings` (0.47.0+) drops the cosmetic warnings array. Branch-scoped since v0.89.0 (issue #649): push consumes the diff's changeset, so configs tracked on another branch's tree are never planned as creates -- they ride along on the result envelope under `orphaned` instead (see `sync diff`). **Since vNEXT (#686)** the manifest baseline `pull_config_hash` is stamped from the API response (or a read-back), not from the files on disk, so a pushed multi-statement SQL transformation -- or anything disabled in the UI whose local YAML lacks `is_disabled` -- no longer shows permanent phantom `REMOTE MODIFIED` drift; if the config cannot be read back after the write the baseline is left UNTOUCHED and a `warnings[]` entry says to run `sync pull` (never a disk-derived fallback). One legacy change is refused per-change with `SYNC_LEGACY_BOUNDARY`: a tree pulled before statement-boundary markers existed whose only difference from the remote is the lost boundaries (pushing it would collapse separate SQL statements into one) -- run `sync pull` for that project first. Ignored components (since vNEXT) are filtered out on both sides of the diff push builds on, so a stale local directory for an ignored component (e.g. `keboola.mcp-server-tool`) is never classified as `DELETED` and can never be pushed as a remote deletion.
 - `sync clone --source DIR --target ALIAS --target-dir DIR [--bucket-map FILE] [--variable-values FILE] [--instance-rename FILE] [--dry-run] [--branch ID]` -- clone a reference synced project into a **fresh** target project and parameterize it (since v0.63.0). Copies the reference tree at `--source` into `--target-dir`, applies declarative overrides from JSON/YAML files (`--bucket-map` `{old_bucket_id: new_bucket_id}` rewrites storage input/output table refs; `--variable-values` `{var_name: value}` overrides `keboola.variables` rows; `--instance-rename` `{old_path_prefix: new_path_prefix}` renames config dirs + manifest paths), re-points the manifest at the target project, and pushes. Because the reference's config ids do not exist in the fresh target, every config is CREATEd fresh and **keboola.flow task `configId`s + transformation variable links are remapped reference->ULID** by push Phase C/D (the push result carries `flow_task_remaps`). **Idempotent**: re-running with an existing `--target-dir` skips copy/overrides and just pushes, reporting `no_changes` / `created: 0`. Fails fast (`CONFIG_ERROR`) if the target already contains the reference's configs -- clone requires a fresh/empty target. `SyncService.clone_project(...)` returns a typed `CloneResult` for in-process SDK callers. Override files must be flat `{id: scalar}` mappings *(since v0.89.0)* -- a nested mapping, list, or null value is rejected with `CONFIG_ERROR` (exit 5) naming the key and its actual type.
-- `sync diff --project ALIAS [--all-projects] [--branch ID]` -- 3-way diff (local vs base vs remote), detects conflicts. `--branch` (0.47.0+) per-invocation dev-branch override. Branch-scoped since v0.89.0 (issue #649): the local side is read from exactly ONE tree (the target branch's subtree, or `main/` when the target has none). Manifest entries belonging to another branch's tree -- what `sync pull --branch <dev>` leaves behind when it re-targets the manifest -- are excluded from the changeset and reported under `orphaned` (`summary.orphaned` + details with `component_id`, `config_id`, `path`, `branch_id`, `branch_path`, `exists_on_target`, `reason`, `hint`); human mode previews the first 10. An orphaned FILE whose `_keboola.config_id` still resolves on the target is adopted (diffed as `unchanged`/`modified`), never re-created; same-tree id claims keep the #482/#497 fork-by-copy CREATE. Fix a non-zero `summary.orphaned` with `sync pull`. Ignored components (since vNEXT) -- `keboola.sandboxes`, `keboola.mcp-server-tool`, and anything listed in the manifest's `ignoredComponents` -- are excluded from BOTH sides of the comparison, so a stale local directory for one of them never shows up as `DELETED`.
+- `sync diff --project ALIAS [--all-projects] [--branch ID]` -- 3-way diff (local vs base vs remote), detects conflicts. `--branch` (0.47.0+) per-invocation dev-branch override. Branch-scoped since v0.89.0 (issue #649): the local side is read from exactly ONE tree (the target branch's subtree, or `main/` when the target has none). Manifest entries belonging to another branch's tree -- what `sync pull --branch <dev>` leaves behind when it re-targets the manifest -- are excluded from the changeset and reported under `orphaned` (`summary.orphaned` + details with `component_id`, `config_id`, `path`, `branch_id`, `branch_path`, `exists_on_target`, `reason`, `hint`); human mode previews the first 10. An orphaned FILE whose `_keboola.config_id` still resolves on the target is adopted (diffed as `unchanged`/`modified`), never re-created; same-tree id claims keep the #482/#497 fork-by-copy CREATE. Fix a non-zero `summary.orphaned` with `sync pull`. **Since vNEXT (#686)** a manifest entry without `metadata.config_hash_version` (written by a pre-vNEXT kbagent) is compared leniently: a stored hash equal to the pre-vNEXT hash of the SAME remote config counts as in sync, so the phantom `codes changed` entries disappear immediately; every other field is still pinned by that hash, so real remote drift is unaffected. One `sync pull` per project stamps the version and ends the leniency. Ignored components (since vNEXT) -- `keboola.sandboxes`, `keboola.mcp-server-tool`, and anything listed in the manifest's `ignoredComponents` -- are excluded from BOTH sides of the comparison, so a stale local directory for one of them never shows up as `DELETED`.
 - `sync status [--directory DIR]` -- show locally modified/added/deleted configs. Also surfaces `plaintext_secret_warnings` (since 0.55.0): in-sync configs/rows whose `#`-secrets are still plaintext on the remote (a leftover from pre-0.54.0 writes; #378). Pending (un-pushed) edits are not flagged. Fix = re-push on >=0.54.0 + rotate (version history keeps the plaintext).
 - `sync branch-link --project ALIAS [--branch-id ID] [--branch-name NAME]` -- link git branch to Keboola dev branch
 - `sync branch-unlink [--directory DIR]` -- remove git-to-Keboola branch mapping