feat(apply): merge sandbox changes into targets with conflict handling #155

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Commit Message: feat(apply): merge sandbox changes into targets with conflict handling
Branch: feature/m1-apply-pipeline

Background

The sandbox merge/apply pipeline merges git worktree and copy-on-write changes into targets with explicit conflict detection and rollback hooks. PlanApplyService is wired to the merge pipeline and persists apply summary fields (files changed, validations run, conflict details). A validation gating hook gathers ValidationAttachments, runs required validations, and blocks apply on failures.

Acceptance Criteria

Implement sandbox merge/apply pipeline for git worktree + copy-on-write strategies with explicit conflict detection and rollback hooks.
Wire PlanApplyService to the merge pipeline and persist apply summary fields (files changed, validations run, conflict details).
Add validation gating hook: gather ValidationAttachments for the plan resources, run required validations, block apply on failures, record results.
Add --allow-empty apply flag behavior aligned with PlanApplyService.guard_empty_changeset.
Ensure apply transitions set terminal states (applied, constrained, errored, cancelled) with error details per spec.

Definition of Done

This issue is complete when:

All subtasks below are completed and checked off.
A Git commit is created where the first line of the commit message matches
the Commit Message in Metadata exactly, followed by a blank line, then
additional lines providing relevant details about the implementation. The
commit body should be appropriate in size for a commit message and relatively
complete in describing what was done.
The commit is pushed to the remote on the branch matching the Branch in
Metadata exactly.
The commit is submitted as a pull request to master, reviewed, and
merged before this issue is marked done.

Subtasks

Implement sandbox merge/apply pipeline for git worktree + copy-on-write strategies with explicit conflict detection and rollback hooks.
Wire PlanApplyService to the merge pipeline and persist apply summary fields (files changed, validations run, conflict details).
Add validation gating hook: gather ValidationAttachments for the plan resources, run required validations, block apply on failures, record results.
Add --allow-empty apply flag behavior aligned with PlanApplyService.guard_empty_changeset.
Ensure apply transitions set terminal states (applied, constrained, errored, cancelled) with error details per spec.
Update docs/reference/plan_apply.md with apply pipeline and conflict outcomes.
Tests (Behave): Add scenarios for apply success, conflict failure, empty changeset guard, and validation-gated apply.
Tests (Robot): Add Robot CLI test covering plan diff + plan apply --yes with sandbox merge and validation output.
Tests (ASV): Add benchmarks/plan_apply_bench.py for apply runtime baseline.
Verify coverage >=97% via nox -s coverage_report. If coverage is <97% then review the current unit test coverage report at build/coverage.xml and use it to write new Behave based unit tests to improve code coverage. Specifically, write Behave style unit tests that are descriptively named and specifically improves coverage on whichever file has the most uncovered lines by writing tests that will target the uncovered lines in the report. Once that is done rerun nox -s coverage_report to verify all tests pass and coverage is above >=97%. Only mark this as complete once coverage is >=97%, if not repeat this task as many times as is needed until coverage reaches >=97%.
Run nox (all default sessions, including benchmark), fix any errors if needed ensuring nox passes across entire code base, do not ignore any failure even if it seems unrelated to this commit, fix it.

Section: #### M1: Minimal Local Source-Code Workflow (Target: Day 7, recovery path)
Status: Open

## Metadata - **Commit Message**: `feat(apply): merge sandbox changes into targets with conflict handling` - **Branch**: `feature/m1-apply-pipeline` ## Background The sandbox merge/apply pipeline merges git worktree and copy-on-write changes into targets with explicit conflict detection and rollback hooks. `PlanApplyService` is wired to the merge pipeline and persists apply summary fields (files changed, validations run, conflict details). A validation gating hook gathers ValidationAttachments, runs required validations, and blocks apply on failures. ## Acceptance Criteria - [ ] Implement sandbox merge/apply pipeline for git worktree + copy-on-write strategies with explicit conflict detection and rollback hooks. - [ ] Wire `PlanApplyService` to the merge pipeline and persist apply summary fields (files changed, validations run, conflict details). - [ ] Add validation gating hook: gather ValidationAttachments for the plan resources, run required validations, block apply on failures, record results. - [ ] Add `--allow-empty` apply flag behavior aligned with `PlanApplyService.guard_empty_changeset`. - [ ] Ensure apply transitions set terminal states (`applied`, `constrained`, `errored`, `cancelled`) with error details per spec. ## Definition of Done This issue is complete when: - All subtasks below are completed and checked off. - A Git commit is created where the **first line** of the commit message matches the Commit Message in Metadata exactly, followed by a blank line, then additional lines providing relevant details about the implementation. The commit body should be appropriate in size for a commit message and relatively complete in describing what was done. - The commit is pushed to the remote on the branch matching the **Branch** in Metadata exactly. - The commit is submitted as a **pull request** to `master`, reviewed, and **merged** before this issue is marked done. ## Subtasks - [ ] Implement sandbox merge/apply pipeline for git worktree + copy-on-write strategies with explicit conflict detection and rollback hooks. - [ ] Wire `PlanApplyService` to the merge pipeline and persist apply summary fields (files changed, validations run, conflict details). - [ ] Add validation gating hook: gather ValidationAttachments for the plan resources, run required validations, block apply on failures, record results. - [ ] Add `--allow-empty` apply flag behavior aligned with `PlanApplyService.guard_empty_changeset`. - [ ] Ensure apply transitions set terminal states (`applied`, `constrained`, `errored`, `cancelled`) with error details per spec. - [ ] Update `docs/reference/plan_apply.md` with apply pipeline and conflict outcomes. - [ ] Tests (Behave): Add scenarios for apply success, conflict failure, empty changeset guard, and validation-gated apply. - [ ] Tests (Robot): Add Robot CLI test covering `plan diff` + `plan apply --yes` with sandbox merge and validation output. - [ ] Tests (ASV): Add `benchmarks/plan_apply_bench.py` for apply runtime baseline. - [ ] Verify coverage >=97% via `nox -s coverage_report`. If coverage is <97% then review the current unit test coverage report at `build/coverage.xml` and use it to write new Behave based unit tests to improve code coverage. Specifically, write Behave style unit tests that are descriptively named and specifically improves coverage on whichever file has the most uncovered lines by writing tests that will target the uncovered lines in the report. Once that is done rerun `nox -s coverage_report` to verify all tests pass and coverage is above >=97%. Only mark this as complete once coverage is >=97%, if not repeat this task as many times as is needed until coverage reaches >=97%. - [ ] Run `nox` (all default sessions, including benchmark), fix any errors if needed ensuring nox passes across **entire** code base, do not ignore any failure even if it seems unrelated to this commit, fix it. **Section**: #### M1: Minimal Local Source-Code Workflow (Target: Day 7, recovery path) **Status**: Open

freemo added this to the v3.0.0 milestone

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#355 Epic: Actor Runtime & Tool Execution (M1)

freemo commented

2026-02-23 18:30:34 +00:00

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Expected completion updated (Day 15 rebaseline): Day 18 / 2026-02-26 (previously Day 17 / 2026-02-25)

**Expected completion updated (Day 15 rebaseline):** Day 18 / 2026-02-26 (previously Day 17 / 2026-02-25)

freemo added the due date 2026-02-23

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#355 Epic: Actor Runtime & Tool Execution (M1)

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#391 Epic: Resource Handlers & Apply Pipeline

freemo referenced this issue

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Epic: Resource Handlers & Apply Pipeline #391

CoreRasurae referenced this issue from a pull request that will close it,

2026-02-25 07:46:46 +00:00

Integration: Validation pipeline, validation-gated apply, diff review, DoD gating, error recovery, and security hardening #417

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#417 Integration: Validation pipeline, validation-gated apply, diff review, DoD gating, error recovery, and security hardening

CoreRasurae referenced this issue from a commit

2026-02-25 10:08:00 +00:00

feat(apply): add validation-gated apply pipeline

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2026-02-25 14:29:10 +00:00

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feat/v3.4.0-acms-lifecycle-policy

pr-9220

fix/a2a-facade-optional-param-validation

feat/ci-guard-llm-secrets

pr-9214

feat/v3.3.0-subplan-status-tracking

feat/v3.3.0-merge-conflict-detection

uat/checkpoint-rollback-merge-tests

fix/pr-review-pool-supervisor-prefix-mismatch

feat/v3.3.0-spawn-subplan-step

auto-time-1-day103-cycle1-session6

feat/v3.8.0-agent-card-endpoint

docs/auto-docs-cycle-24-showcase-nav

auto-inf-3-consolidate-behave-fixtures

fix/issue-7663-docs-writer-missing

auto-time-1-day103-cycle2

docs/timeline-day-104-auto-time-1

auto-arch-16/spec-xml-prompt-injection-mitigation

bugfix/m4-invariant-persistence

uat-a2a-facade-tests-v350

bugfix/m3-behave-parallel-failed-chunk-logs

bugfix/7664-automation-tracking-label-requirements

docs/auto-time-1-timeline-update-2026-04-14

docs/auto-docs-1-milestone-v3-updates

fix/issue-6344-plan-execute-rich-output

docs/action-config-schema-api

fix/bug-hunt-supervisor-nonexistent-file-preflight

fix/retry-policy-model-missing-fields

docs/validation-gate-empty-run-guard

auto-arch-15/spec-retry-policy-canonical-fields

docs/lockservice-advisory-locking

docs/changelog-plan-fix-4197

spec/milestone-plan-section

docs/update-changelog-recent-features

fix/test-infra-remove-redundant-python-variable-robot-files

timeline/day-104-2026-04-14-cycle2

fix/bdd-feature-file-tags

auto-arch-13/spec-default-automation-profile

docs/auto-docs-cycle-1-2026-04-12

docs/cycle-1-git-worktree-sandbox

spec/architecture-critical-gap-fixes

docs/timeline-day-104-auto-time-2

auto-arch-1/add-v380-v390-milestone-plan

docs/developer-setup-guide

fix/auto-profile-spec-prose-description

auto-arch-10/spec-tui-a2a-integration-layer

spec/resource-event-types-clarification

auto-docs-4/changelog-and-observability

auto-arch-4/adr-049-layered-boundary-enforcement

docs/a2a-protocol-autonomy-hardening

auto-arch-9/spec-v3.8.0-milestone-plan

docs/auto-docs-3-reference-index

auto-arch-7/spec-apply-git-worktree

docs/timeline-day104-cycle1-auto-time-4

docs/auto-docs-cycle-1-changelog-updates

auto-arch-6/adr-049-spec-restructuring

docs/auto-docs-1-v340-acms-context-management

docs/auto-docs-1-v320-v330-cli-reference

auto-arch-5/v3.9.0-milestone-plan

test/create-scripts

auto-time-1-day104

timeline/day-104-2026-04-14

docs/auto-time-4-day103-cycle5

auto-time-3-day103-cycle4

auto-docs-5-architecture-overview

spec/three-way-merge-strategy-v3.3.0

spec/checkpoint-system-v3.3.0

auto-docs-4-api-docs-update

auto-docs-1-changelog-expansion

spec/invariant-management-system-v3.2.0

pr-8289

spec/plan-correction-engine-v3.2.0

spec/layered-architecture-boundary-policy

spec/tui-materializer-a2a-integration-v3.7.0

spec/decision-recording-system-v3.2.0

docs/auto-docs-1-milestone-overview

pr-7484

pr-4212

auto-arch-3/v3.8.0-milestone-plan

auto-docs-6/troubleshooting-and-config

auto-time-1-day103-session5

auto-docs-5/contributor-guide-and-readme

docs/plan-tree-ulid-examples

docs/m3-spec-clarify-path-datetime-plugin-contracts

docs/auto-docs-cycle-10-diagnostics-ref

auto-docs-3/user-guide-and-architecture

docs/cycle-7-changelog-update

spec/reconciliation-failure-behavior

auto-docs-2/api-documentation

auto-arch-2/adr-053-repositories-decomposition

auto-docs-1/release-notes-v3.0-v3.1

spec/update-validation-attach-project-delete

spec/architecture-cycle2-impl-clarifications

auto-arch-1/adr-049-052-violations

auto-time-1-day103

docs/auto-docs-cycle-13-updates

docs/timeline-day-102-auto-time

timeline/day-103-2026-04-13

spec/arch-invariant-cli-completeness

spec/update-cycle1-validation-attach-project-delete

docs/add-session-management-showcase

spec/arch-sandbox-path-correction-cycle9

spec/architecture-v380-milestone-plan

docs/auto-docs-cycle-12-updates

docs/cycle-1-validation-gate-fix

docs/2026-04-08-unreleased-changelog

docs/auto-docs-cycle-2-2026-04-10

docs/session-4615-2026-04-08-cycle1

feat/issue-6361-shell-safety-service-tui

spec/architecture-cycle-25-new-features

fix/issue-6345-automation-profile-add-output

docs/timeline-day-102-2026-04-12

docs/cycle-2-git-worktree-acms-hydrator

spec/arch-sandbox-cleanup-discovery

docs/timeline-day96-2026-04-08

docs/auto-docs-cycle-11

spec/fix-sandbox-strategy-protocol-name

spec/arch-acms-tier-hydration

fix/v3.4.0/context-settings-defaults

docs/add-example-repl-and-actor-run

docs/auto-docs-cycle-10-updates

docs/session-4-2026-04-08-updates

docs/showcase-all-examples-consolidated

docs/timeline-day-97

docs/acms-context-hydrator-cycle2

docs/add-example-output-format-flags

spec/arch-failfast-cancel-semantics

timeline/day-101-2026-04-11

docs/timeline-day99-2026-04-09-v2

docs/auto-docs-cycle-2-worktree-acms

spec/architecture-v3.8.0-milestone-plan

docs/api-lsp-acms-reference

improvement/agent-bug-hunt-pool-supervisor-yaml-syntax-fix

spec/project-delete-deleted-at-field

spec/architecture-provider-registry-tui-materializer

spec/document-reconciliation-blocked-error-5942

fix/issue-7482-git-log-injection

spec/devcontainer-auto-discovery-schema

feat/issue-6350-conversation-content-pruning

docs/update-module-guides-2026-04-10

timeline/day-100-2026-04-10-auto-time-cycle1

timeline/day-99-2026-04-09-auto-time-v2

docs/cycle-3-module-guides

timeline/day-99-2026-04-09-auto-time

pr-4226

spec/additional-llm-providers-gemini-groq-cohere-together-ollama-mistral

spec/document-context-tier-hydrator-6175

docs/timeline-day99-2026-04-09

spec/invariant-cli-clarifications

docs/add-example-project-init-and-context-management

spec/reconciliation-blocked-error-documentation

spec/fix-invariant-precedence-reference-5861

spec/fix-plan-correct-accepts-plan-id-5558

spec/fix-validation-attach-synopsis-5328

docs/timeline-day-99-cycle-1

docs/timeline-day-99-cycle-2

fix/actor-context-list-regex-arg

docs/timeline-day-99-cycle-3

spec/arch-security-mode-init

docs/auto-docs-cycle-9-updates

fix-resource-fix-resource-remove-to-check-correct-edge-table

feat/issue-6434-tui-env-var-expansion

fix/issue-6321-plan-prompt-timing-field

fix/issue-6322-resource-add-url-flag

feat/issue-6348-sessions-screen

spec/plan-show-command

temp

feat/harden-label-restrictions-1775753628

spec/invariant-reconciliation-failure-behavior

spec/add-reconciliation-failure-behavior-5942

spec/architecture-corrections-cycle3

spec/checkpoint-trigger-names-and-config-key-fix

spec/fix-ai-provider-interface-5801

spec/azure-api-version-default-update

docs/auto-docs-writer-cycle1-labels

spec/fix-resource-type-yaml-format-5622

spec/add-plan-revert-resume-commands-5574

docs/auto-docs-cycle-1-2026-04-09

spec/plan-correct-plan-id-or-decision-id-5558

spec/fix-subgraph-node-actor-ref-field-5427

issue/5284-master-ci-fix

timeline/day-99-2026-04-09-v2

merge-me

docs/session-3377-initial-docs-update

fix/llm-provider-subpackage-exports

spec/arce-acronym-and-tui-keybinding-fixes

spec/architecture-corrections-cycle2

spec/architecture-corrections-cycle1

docs/cycle-1-updates

spec/tui-clarifications-session-export-persona

docs/session-4940-2026-04-08-cycle1

spec/architecture-milestone-plan-v3.2-v3.7

docs/session-4743-2026-04-08-cycle1

docs/timeline-day-98

fix/plan-lifecycle-service-rollback-method

docs/timeline-day98-2026-04-08-v2

docs/add-example-action-and-plan-management

docs/session-2026-04-06-updates

docs/ca-docs-writer-v3.8.1-2026-04-05

fix/session-tell-stub-missing-panels-and-actor-execution

improvement/agent-arch-guard-clone-failure-handling

improvement/agent-test-infra-health-spam-fix-v2

fix-tdd-invert-non-assertion-exceptions

improvement/agent-arch-guard-clone-failure

bugfix/3472-fix-tdd-inversion-logic

bugfix/989-fix-persistence-json-decode-error

improvement/agent-supervisor-tracking-labels-v2

docs/timeline-day95-v2

docs/timeline-day95-final

docs/update-lsp-api-and-changelog

fix/lsp-resource-handler-module-missing

docs/timeline-day95-final-2026-04-05

fix/a2a-plan-correct-rollback-wiring

docs/add-lsp-api-and-changelog-2026-04-05

fix/tool-registry-validation-type-discriminator

docs/v3.7.0-documentation-update

docs/ca-docs-writer-2026-04-05-cycle2

fix/invariant-set-merge-action-scope

docs/unreleased-feature-docs

fix/concurrency-cost-tracker-record-usage-race-condition

improvement/agent-ca-test-infra-improver-failure-handling

docs/update-changelog-mcp-plan-ci-2026-04-05

improvement/agent-pr-reviewer-milestone-prioritization

docs/timeline-day95-refresh-2026-04-05

improvement/agent-mandatory-labels-tracking-issues

docs/api-domain-providers-changelog-2026-04-05

docs/ca-docs-writer-2026-04-05

docs/timeline-day95-refresh

fix/skill-add-include-validation

docs/timeline-day-95-2026-04-05-update3

docs/timeline-day-95-2026-04-05-update2

docs/ci-incident-runbook-2597

improvement/agent-ca-test-infra-improver-worker-api-mode

docs/shell-safety-api-and-readme-highlights

docs/timeline-day-55-2026-04-04-v2

docs/timeline-day-55-2026-04-04

docs/timeline-day54-update3

improvement/agent-ca-test-infra-improver-fixes

spec/restructure-monolithic-to-split

docs/timeline-day54-update-v2

docs/timeline-day54-update

fix-agents

docs/shell-safety-and-domain-base-model

fix/1452-impl

fix/1473-plan-cancel

fix/1425-test

fix/1426-config

fix/1421-perf

fix/1424-impl

test/int-wf16-devcontainer

feature/m8-tui-persona-export

feature/m7-post-resource-equivalence

test/e2e-m4-acceptance

feature/m6-tantivy-backend

feature/m6-estimation

feature/m6-estimation-report-model

feature/observability-prometheus-audit

feat/server-auth-namespace

feature/m8-session-editing

feature/llm-actor-subplan-wiring

feature/m8-tui-first-run-actor-selection

feature/m8-tui-conversation-block-catalog

feature/m8-tui-settings-screen

feature/m7-e2e-porting

feature/m6-estimation-historical-stats

feature/m8-tui-persona-export-import

feature/m8-tui-sessions-screen

feature/m7-graph-backend

feature/m8-tui-block-context-menu

feature/m8-tui-tool-call-expand

feature/m4-missing-builtin-tools

docs/v3.7.0-release-docs

feature/m8-tui-session-export

test/e2e-wf15-disaster-recovery

test/e2e-wf03-refactoring

test/e2e-m3-acceptance

feature/m8-tui-prompt-history

feature/m8-tui-actor-thought-block-rendering

bugfix/m6-build-hierarchy-child-ids

feature/resource-inheritance-wiring

test/e2e-wf09-session

test/e2e-wf06-doc-generation

test/e2e-wf08-cloud-infra

test/e2e-wf02-test-generation

test/e2e-wf13-custom-profile

test/e2e-wf11-graph-actor

test/e2e-wf01-hello-world

test/int-wf17-explicit-container

test/int-wf12-hierarchical

test/int-wf15-disaster-recovery

test/int-wf13-custom-profile

test/int-wf03-refactoring

test/int-wf11-graph-actor

test/int-wf10-batch

test/int-wf09-session

feature/m3-tdd-issue-consistency-gate

feature/m3-invariant-enforcement-strategize

test/int-wf18-container-clone

test/int-wf01-hello-world

feature/m6-diagnostic-dashboard-health-categories

feature/m6-cli-polish

fix/e2e-db-isolation

feature/m7-post-tui

feature/m9-asgi-endpoint

feature/m7-post-server

tdd/m7-audit-session-race

tdd/m3-skill-add-regression

feature/m9-remote-repos

feature/fs-mount-file-types

tdd/container-resolve-crash

test/e2e-m1-acceptance

test/e2e-m2-acceptance

eugen.thaci-patch-3

eugen.thaci-patch-2

eugen.thaci-patch-1

aditya-fix-latest

feature/m4-secret-masking-llm-context

aditya-fix

refactor/m3-replace-mktemp

refactor/m3-remove-unittest-mock-integration

refactor/m3-remove-robot-mock-imports

refactor/m3-remove-mock-llm-integration

docs/improved-menu-adr

feature/m7-post-auth

feature/m3-fix-resource-bootstrap

feature/post-safety-profile-tests

integration/batch-2026-03-02

feat/slipcover

docs/safety-profile-spec-composition

integrate/freemo-batch-1

feature/m4-error-recovery

feature/m4-security-template

feature/m3-validation-pipeline

develop-aditya-2

feature/m3-diff-review

feature/m3-validation-apply

feature/m6-acp-stubs

feature/m4-correction-flows

feature/m1-plan-execute-runtime

feature/m4-security-exceptions

feature/m4-definition-of-done

feature/m4-correction-model

feature/m1-apply-pipeline

feature/m5-automation-profiles

feature/m2-lsp-stubs

feature/m3-invariants

feature/m1-actor-runtime

feature/docs-v2-restore

feature/m6-perf-scale

feature/m6-validation-edge

feature/m3-session-cli

feature/m1-persistence-tests-robot

feature/m3-config-cli

feature/m1-cli-tests-robot

feature/m5-subplan-tests

feature/m6-review-playbook

feature/aditya-m3-actor-loader

feature/m3-skill-protocol

feature/m4-automation-legacy-cleanup

feature/m3-change-model

feature/m3-skill-git

feature/m3-skill-registry

feature/m4-security-eval

fix/robot-tests

feature/m3-actor-registry

feature/m3-tool-cli

feature/m4-automation-profiles-cli

feature/m2-resource-cli-extensions

feature/m3-actor-loader

feature/m3-tool-domain-robot

feature/m3-skill-domain-robot

feature/m3-skill-cli

feature/m1-resource-db-robot-tests

feature/m3-session-domain-robot

feature/m1-persistence-tests

feature/m1-cli-tests

ten-branches-backup

feature/m3-skill-schema

feature/m3-session-persistence

feature/automation-profiles-and-resource-dag

feature/m1-plan-repo

feature/m1-db-plan-phase-rebaseline

feat/B4-sandbox

feat/B2-cli-wiring

feat/B5-project-persistence

feat/B1-project-data-models

feat/b1-data-models

feat-repo-manager-and-sourcegraph-support

feat/actor-schema

fix/component-isolation-security-fix

feat/ontology-agent

fix/error-handling-security-fix

fix/concurrency-security-fix

fix/serialization-security-fix

fix/server-side-request-forgery-security-fix

fix/file-system-security

fix/template-injection-fix

fix/data-injection-fix

tests/unit-tests

latest/poetry-generator

poetry-generator

config/contract-metadata-extractor

docs/readme-yaml-syntax

config/memory-yaml

fix/double-response

brent-additions

intel_2_demo

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auto-working-v6

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auto-before-rewrite-v0

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