fix(jira): select open ticket before closing

Codex-Session: codex resume 01a1c1de-e73c-7622-949e-fbbbd741b6c5

README.md

@@ -167,6 +167,7 @@ TEMPLATES:
    -wurl, -workflow-url string[]          workflow url or list containing workflow urls to run (comma-separated, file)
    -validate                              validate the passed templates to nuclei
    -plan string                           write the work a scan would do with its estimated cost to a jsonl file, then exit without sending requests to any target
+   -run-plan string                       run only the entries of a -plan file, logging finished ones to <file>.done so running it again resumes
    -nss, -no-strict-syntax                disable strict syntax check on templates
    -td, -template-display                 displays the templates content
    -tl                                    list all templates matching current filters

README_CN.md

@@ -165,6 +165,7 @@ TEMPLATES:
    -wurl, -workflow-url string[]          workflow url or list containing workflow urls to run (comma-separated, file)
    -validate                              validate the passed templates to nuclei
    -plan string                           write the work a scan would do with its estimated cost to a jsonl file, then exit without sending requests to any target
+   -run-plan string                       run only the entries of a -plan file, logging finished ones to <file>.done so running it again resumes
    -nss, -no-strict-syntax                disable strict syntax check on templates
    -td, -template-display                 displays the templates content
    -tl                                    list all templates matching current filters

README_ES.md

@@ -165,6 +165,7 @@ TEMPLATES:
    -wurl, -workflow-url string[]          workflow url or list containing workflow urls to run (comma-separated, file)
    -validate                              validate the passed templates to nuclei
    -plan string                           write the work a scan would do with its estimated cost to a jsonl file, then exit without sending requests to any target
+   -run-plan string                       run only the entries of a -plan file, logging finished ones to <file>.done so running it again resumes
    -nss, -no-strict-syntax                disable strict syntax check on templates
    -td, -template-display                 displays the templates content
    -tl                                    list all templates matching current filters

README_FA.md

@@ -182,6 +182,7 @@ TEMPLATES:
    -wurl, -workflow-url string[]          workflow url or list containing workflow urls to run (comma-separated, file)
    -validate                              validate the passed templates to nuclei
    -plan string                           write the work a scan would do with its estimated cost to a jsonl file, then exit without sending requests to any target
+   -run-plan string                       run only the entries of a -plan file, logging finished ones to <file>.done so running it again resumes
    -nss, -no-strict-syntax                disable strict syntax check on templates
    -td, -template-display                 displays the templates content
    -tl                                    list all templates matching current filters

README_ID.md

@@ -165,6 +165,7 @@ TEMPLATES:
    -wurl, -workflow-url string[]          workflow url or list containing workflow urls to run (comma-separated, file)
    -validate                              validate the passed templates to nuclei
    -plan string                           write the work a scan would do with its estimated cost to a jsonl file, then exit without sending requests to any target
+   -run-plan string                       run only the entries of a -plan file, logging finished ones to <file>.done so running it again resumes
    -nss, -no-strict-syntax                disable strict syntax check on templates
    -td, -template-display                 displays the templates content
    -tl                                    list all templates matching current filters

README_JP.md

@@ -165,6 +165,7 @@ TEMPLATES:
    -wurl, -workflow-url string[]          workflow url or list containing workflow urls to run (comma-separated, file)
    -validate                              validate the passed templates to nuclei
    -plan string                           write the work a scan would do with its estimated cost to a jsonl file, then exit without sending requests to any target
+   -run-plan string                       run only the entries of a -plan file, logging finished ones to <file>.done so running it again resumes
    -nss, -no-strict-syntax                disable strict syntax check on templates
    -td, -template-display                 displays the templates content
    -tl                                    list all templates matching current filters

README_KR.md

@@ -165,6 +165,7 @@ TEMPLATES:
    -wurl, -workflow-url string[]          workflow url or list containing workflow urls to run (comma-separated, file)
    -validate                              validate the passed templates to nuclei
    -plan string                           write the work a scan would do with its estimated cost to a jsonl file, then exit without sending requests to any target
+   -run-plan string                       run only the entries of a -plan file, logging finished ones to <file>.done so running it again resumes
    -nss, -no-strict-syntax                disable strict syntax check on templates
    -td, -template-display                 displays the templates content
    -tl                                    list all templates matching current filters

README_PT-BR.md

@@ -165,6 +165,7 @@ TEMPLATES:
    -wurl, -workflow-url string[]          workflow url or list containing workflow urls to run (comma-separated, file)
    -validate                              validate the passed templates to nuclei
    -plan string                           write the work a scan would do with its estimated cost to a jsonl file, then exit without sending requests to any target
+   -run-plan string                       run only the entries of a -plan file, logging finished ones to <file>.done so running it again resumes
    -nss, -no-strict-syntax                disable strict syntax check on templates
    -td, -template-display                 displays the templates content
    -tl                                    list all templates matching current filters

README_TR.md

@@ -165,6 +165,7 @@ TEMPLATES:
    -wurl, -workflow-url string[]          workflow url or list containing workflow urls to run (comma-separated, file)
    -validate                              validate the passed templates to nuclei
    -plan string                           write the work a scan would do with its estimated cost to a jsonl file, then exit without sending requests to any target
+   -run-plan string                       run only the entries of a -plan file, logging finished ones to <file>.done so running it again resumes
    -nss, -no-strict-syntax                disable strict syntax check on templates
    -td, -template-display                 displays the templates content
    -tl                                    list all templates matching current filters

cmd/nuclei/main.go

@@ -314,6 +314,7 @@ on extensive configurability, massive extensibility and ease of use.`)
 		flagSet.StringSliceVarP(&options.WorkflowURLs, "workflow-url", "wurl", nil, "workflow url or list containing workflow urls to run (comma-separated, file)", goflags.FileCommaSeparatedStringSliceOptions),
 		flagSet.BoolVar(&options.Validate, "validate", false, "validate the passed templates to nuclei"),
 		flagSet.StringVar(&options.PlanFile, "plan", "", "write the work a scan would do with its estimated cost to a jsonl file, then exit without sending requests to any target"),
+		flagSet.StringVar(&options.RunPlanFile, "run-plan", "", "run only the entries of a -plan file, logging finished ones to <file>.done so running it again resumes"),
 		flagSet.BoolVarP(&options.NoStrictSyntax, "no-strict-syntax", "nss", false, "disable strict syntax check on templates"),
 		flagSet.BoolVarP(&options.TemplateDisplay, "template-display", "td", false, "displays the templates content"),
 		flagSet.BoolVar(&options.TemplateList, "tl", false, "list all templates matching current filters"),

internal/runner/options.go

@@ -558,18 +558,31 @@ func getBoolEnvValue(key string) bool {
 // validatePlanOptions rejects options that change the templates or targets
 // only once scanning starts, which a plan written beforehand cannot show.
 func validatePlanOptions(options *types.Options) error {
-	if options.PlanFile == "" {
+	if options.RunPlanFile != "" && options.PlanFile != "" {
+		return errors.New("-plan cannot be used with -run-plan")
+	}
+	if options.RunPlanFile != "" && options.Resume != "" {
+		return errors.New("-run-plan cannot be used with -resume, the plan's done log resumes it")
+	}
+	if options.PlanFile == "" && options.RunPlanFile == "" {
 		return nil
 	}
+	// -automatic-scan builds its own engine, so a plan set on the main engine
+	// would never be consulted. The other flags change the targets only after
+	// a plan has been written.
+	flag := "-plan"
+	if options.PlanFile == "" {
+		flag = "-run-plan"
+	}
 	switch {
 	case options.AutomaticScan:
-		return errors.New("-plan cannot be used with -automatic-scan, which picks templates while scanning")
+		return fmt.Errorf("%s cannot be used with -automatic-scan, which picks templates while scanning", flag)
 	case options.Uncover || len(options.UncoverQuery) > 0:
-		return errors.New("-plan cannot be used with -uncover, which finds targets over the network")
+		return fmt.Errorf("%s cannot be used with -uncover, which finds targets over the network", flag)
 	case options.PreflightPortScan:
-		return errors.New("-plan cannot be used with -preflight-portscan, which drops targets after scanning their ports")
+		return fmt.Errorf("%s cannot be used with -preflight-portscan, which drops targets after scanning their ports", flag)
 	case options.DASTServer || options.DASTProxy:
-		return errors.New("-plan cannot be used with -dast-server or -dast-proxy, which start a server instead of writing a plan")
+		return fmt.Errorf("%s cannot be used with -dast-server or -dast-proxy, which start a server instead of writing a plan", flag)
 	}
 	return nil
 }

internal/runner/plan_options_test.go

@@ -23,4 +23,19 @@ func TestPlanRejectsOptionsThatChangeTargetsLater(t *testing.T) {
 	require.NoError(t, validatePlanOptions(&types.Options{Uncover: true}), "only -plan restricts them")
 	require.NoError(t, validatePlanOptions(&types.Options{UncoverQuery: goflags.StringSlice{"example"}}))
 	require.NoError(t, validatePlanOptions(&types.Options{DASTServer: true}))
+
+	require.Error(t, validatePlanOptions(&types.Options{RunPlanFile: "p", PlanFile: "q"}))
+	require.Error(t, validatePlanOptions(&types.Options{RunPlanFile: "p", Resume: "r"}))
+	require.NoError(t, validatePlanOptions(&types.Options{RunPlanFile: "p"}))
+
+	for name, options := range map[string]*types.Options{
+		"run automatic scan": {RunPlanFile: "p", AutomaticScan: true},
+		"run uncover":        {RunPlanFile: "p", Uncover: true},
+		"run uncover query":  {RunPlanFile: "p", UncoverQuery: goflags.StringSlice{"example"}},
+		"run preflight":      {RunPlanFile: "p", PreflightPortScan: true},
+		"run dast server":    {RunPlanFile: "p", DASTServer: true},
+		"run dast proxy":     {RunPlanFile: "p", DASTProxy: true},
+	} {
+		require.Error(t, validatePlanOptions(options), name)
+	}
 }

internal/runner/run_plan.go

@@ -0,0 +1,215 @@
+package runner
+
+import (
+	"bufio"
+	"bytes"
+	"fmt"
+	"io"
+	"os"
+	"strconv"
+	"sync"
+
+	"github.com/projectdiscovery/nuclei/v3/pkg/utils/json"
+)
+
+// planRun limits a scan to the entries of a plan file and appends the id of
+// each finished entry to the plan's done log, so running the plan again skips
+// them. Ids are derived from what an entry runs, not from its position, so the
+// log still applies after the plan is written again for changed targets or
+// templates.
+type planRun struct {
+	mu      sync.Mutex
+	entries map[uint64]plannedEntry
+	// done holds finished origin groups by the id of their first entry; an
+	// entry outside a group is its own group
+	done   map[uint64]struct{}
+	log    *os.File
+	logErr error
+	// resumed counts the entries finished before this run
+	resumed int
+}
+
+type plannedEntry struct {
+	group uint64
+	seen  bool
+}
+
+func planDoneLog(planFile string) string {
+	return planFile + ".done"
+}
+
+func openPlanRun(planFile string) (*planRun, error) {
+	run := &planRun{entries: make(map[uint64]plannedEntry), done: make(map[uint64]struct{})}
+	if err := run.readPlan(planFile); err != nil {
+		return nil, err
+	}
+	if err := run.readDoneLog(planDoneLog(planFile)); err != nil {
+		return nil, err
+	}
+	log, err := os.OpenFile(planDoneLog(planFile), os.O_CREATE|os.O_RDWR|os.O_APPEND, 0o644)
+	if err != nil {
+		return nil, err
+	}
+	// an interrupted write leaves a partial line, which the next id must not
+	// extend
+	if info, err := log.Stat(); err == nil && info.Size() > 0 {
+		last := make([]byte, 1)
+		if _, err := log.ReadAt(last, info.Size()-1); err == nil && last[0] != '\n' {
+			_, _ = log.WriteString("\n")
+		}
+	}
+	run.log = log
+	return run, nil
+}
+
+func (run *planRun) readPlan(planFile string) error {
+	file, err := os.Open(planFile)
+	if err != nil {
+		return err
+	}
+	defer func() { _ = file.Close() }()
+	reader := bufio.NewReader(file)
+	for number := 1; ; number++ {
+		line, readErr := reader.ReadBytes('\n')
+		if line = bytes.TrimSpace(line); len(line) > 0 {
+			var entry struct {
+				ID            string `json:"id"`
+				AlternativeTo string `json:"alternative-to"`
+			}
+			if err := json.Unmarshal(line, &entry); err != nil {
+				return fmt.Errorf("%s:%d: %w", planFile, number, err)
+			}
+			// the summary line has no id
+			if entry.ID != "" {
+				id, ok := parsePlanID(entry.ID)
+				if !ok {
+					return fmt.Errorf("%s:%d: invalid id %q", planFile, number, entry.ID)
+				}
+				group := id
+				if entry.AlternativeTo != "" {
+					if group, ok = parsePlanID(entry.AlternativeTo); !ok {
+						return fmt.Errorf("%s:%d: invalid alternative-to %q", planFile, number, entry.AlternativeTo)
+					}
+				}
+				run.entries[id] = plannedEntry{group: group}
+			}
+		}
+		if readErr == io.EOF {
+			return nil
+		}
+		if readErr != nil {
+			return readErr
+		}
+	}
+}
+
+func (run *planRun) readDoneLog(path string) error {
+	file, err := os.Open(path)
+	if os.IsNotExist(err) {
+		return nil
+	}
+	if err != nil {
+		return err
+	}
+	defer func() { _ = file.Close() }()
+	scanner := bufio.NewScanner(file)
+	for scanner.Scan() {
+		// a partial line from an interrupted write does not parse and is
+		// run again
+		id, ok := parsePlanID(scanner.Text())
+		if !ok {
+			continue
+		}
+		if entry, planned := run.entries[id]; planned {
+			run.done[entry.group] = struct{}{}
+		}
+	}
+	if err := scanner.Err(); err != nil {
+		return err
+	}
+	for _, entry := range run.entries {
+		if _, done := run.done[entry.group]; done {
+			run.resumed++
+		}
+	}
+	return nil
+}
+
+// parsePlanID keeps ids as integers, which a plan of millions of entries
+// holds in a fraction of the memory of strings.
+func parsePlanID(id string) (uint64, bool) {
+	if len(id) != 16 {
+		return 0, false
+	}
+	value, err := strconv.ParseUint(id, 16, 64)
+	return value, err == nil
+}
+
+func (run *planRun) Skip(id string) bool {
+	key, ok := parsePlanID(id)
+	if !ok {
+		return true
+	}
+	run.mu.Lock()
+	defer run.mu.Unlock()
+	entry, planned := run.entries[key]
+	if !planned {
+		return true
+	}
+	if !entry.seen {
+		entry.seen = true
+		run.entries[key] = entry
+	}
+	_, done := run.done[entry.group]
+	return done
+}
+
+func (run *planRun) Finished(id string) {
+	key, ok := parsePlanID(id)
+	if !ok {
+		return
+	}
+	run.mu.Lock()
+	defer run.mu.Unlock()
+	entry, planned := run.entries[key]
+	if !planned {
+		return
+	}
+	run.done[entry.group] = struct{}{}
+	// written straight to the file: ctrl+c exits without running defers
+	if _, err := run.log.WriteString(id + "\n"); err != nil && run.logErr == nil {
+		run.logErr = err
+	}
+}
+
+// unreached counts unfinished entries the scan did not get to: those of a
+// host it found unresponsive, and those it does not have because it runs
+// with other templates, targets or options than the plan.
+func (run *planRun) unreached() int {
+	run.mu.Lock()
+	defer run.mu.Unlock()
+	count := 0
+	for _, entry := range run.entries {
+		if _, done := run.done[entry.group]; !done && !entry.seen {
+			count++
+		}
+	}
+	return count
+}
+
+func (run *planRun) close() error {
+	if err := run.log.Close(); err != nil && run.logErr == nil {
+		run.logErr = err
+	}
+	return run.logErr
+}
+
+// finishPlanRun closes the done log and reports the entries left to run.
+func (r *Runner) finishPlanRun(run *planRun) {
+	if err := run.close(); err != nil {
+		r.Logger.Error().Msgf("Could not write %s: %s", planDoneLog(r.options.RunPlanFile), err)
+	}
+	if unreached := run.unreached(); unreached > 0 {
+		r.Logger.Info().Msgf("%d plan entries did not run; running the plan again retries them. Entries run only when the scan has the templates, targets and options the plan was written with", unreached)
+	}
+}

internal/runner/run_plan_test.go

@@ -0,0 +1,52 @@
+package runner
+
+import (
+	"os"
+	"path/filepath"
+	"testing"
+
+	"github.com/stretchr/testify/require"
+)
+
+func TestPlanRunResumesFromItsDoneLog(t *testing.T) {
+	planFile := filepath.Join(t.TempDir(), "plan.jsonl")
+	require.NoError(t, os.WriteFile(planFile, []byte(`{"id":"00000000000000a1","target":"https://a.example/x","templates":["root"]}
+{"id":"00000000000000a2","target":"https://a.example/y","templates":["root"],"alternative-to":"00000000000000a1"}
+{"id":"00000000000000b1","target":"https://b.example","templates":["generic"]}
+{"id":"00000000000000c1","target":"https://c.example","templates":["generic"]}
+{"summary":{"entries":3,"alternatives":1}}
+`), 0o644))
+	// the last line was cut off by an interrupted write
+	require.NoError(t, os.WriteFile(planDoneLog(planFile), []byte("00000000000000b1\n00000000"), 0o644))
+
+	run, err := openPlanRun(planFile)
+	require.NoError(t, err)
+	require.Len(t, run.entries, 4)
+	require.Equal(t, 1, run.resumed)
+
+	require.True(t, run.Skip("00000000000000b1"), "finished in the previous run")
+	require.True(t, run.Skip("00000000000000ff"), "not in the plan")
+	require.False(t, run.Skip("00000000000000a1"))
+	run.Finished("00000000000000a1")
+	require.True(t, run.Skip("00000000000000a2"), "its origin is covered")
+	require.Equal(t, 1, run.unreached(), "c1 never ran")
+	require.NoError(t, run.close())
+
+	log, err := os.ReadFile(planDoneLog(planFile))
+	require.NoError(t, err)
+	require.Equal(t, "00000000000000b1\n00000000\n00000000000000a1\n", string(log), "the partial line is not extended")
+
+	again, err := openPlanRun(planFile)
+	require.NoError(t, err)
+	require.Equal(t, 3, again.resumed, "b1, and a1 with its alternative")
+	require.True(t, again.Skip("00000000000000a2"), "a finished origin stays covered")
+	require.False(t, again.Skip("00000000000000c1"))
+	require.NoError(t, again.close())
+}
+
+func TestPlanRunRejectsAMalformedPlan(t *testing.T) {
+	planFile := filepath.Join(t.TempDir(), "plan.jsonl")
+	require.NoError(t, os.WriteFile(planFile, []byte("{\"id\":\"00000000000000a1\"}\nnot json\n"), 0o644))
+	_, err := openPlanRun(planFile)
+	require.ErrorContains(t, err, "plan.jsonl:2")
+}

internal/runner/runner.go

@@ -855,6 +855,15 @@ func (r *Runner) RunEnumeration() error {
 			}
 		}()
 	}
+	if r.options.RunPlanFile != "" {
+		run, err := openPlanRun(r.options.RunPlanFile)
+		if err != nil {
+			return errors.Wrap(err, "could not read plan")
+		}
+		r.Logger.Info().Msgf("Running %d plan entries from %s, %d already finished", len(run.entries), r.options.RunPlanFile, run.resumed)
+		executorEngine.SetPlanRun(run)
+		defer r.finishPlanRun(run)
+	}
 	// TODO: remove below functions after v3 or update warning messages
 	templates.PrintDeprecatedProtocolNameMsgIfApplicable(r.options.Silent, r.options.Verbose)
 

pkg/core/engine.go

@@ -51,6 +51,7 @@ type Engine struct {
 	executerOpts              *protocols.ExecutorOptions
 	Callback                  func(*output.ResultEvent) // Executed on results
 	templateExecutionCallback TemplateExecutionCallback
+	planRun                   PlanRun
 	Logger                    *gologger.Logger
 }
 

pkg/core/executors.go

@@ -36,9 +36,13 @@ func (e *Engine) executeAllSelfContained(ctx context.Context, alltemplates []*te
 			if sharedBudget {
 				defer e.options.ReleaseTemplateThread()
 			}
+			defer e.tasksDone(1)
+			planned, skip := e.claimPlanned(template, &contextargs.MetaInput{})
+			if skip {
+				return
+			}
 			finished := e.templateExecutionStarted(template, "")
 			defer func() { finished(ctx.Err()) }()
-			defer e.tasksDone(1)
 			var err error
 			var match bool
 			ctx := scan.NewScanContext(ctx, contextargs.New(ctx))
@@ -55,6 +59,8 @@ func (e *Engine) executeAllSelfContained(ctx context.Context, alltemplates []*te
 			}
 			if err != nil {
 				e.options.Logger.Warning().Msgf("[%s] Could not execute step (self-contained): %s\n", e.executerOpts.Colorizer.BrightBlue(template.ID), err)
+			} else if ctx.Context().Err() == nil {
+				planned()
 			}
 			results.CompareAndSwap(false, match)
 		}(v, usesSharedTemplateBudget)
@@ -330,6 +336,16 @@ func (e *Engine) tasksDone(count int64) {
 func (e *Engine) executeTemplateOnInput(ctx context.Context, template *templates.Template, value *contextargs.MetaInput) (matched bool, err error) {
 	// a pair skipped as a repeat of its origin is done as well
 	defer e.tasksDone(1)
+	planned, skip := e.claimPlanned(template, value)
+	if skip {
+		return false, nil
+	}
+	// an origin a sibling already covered is settled too, so it is recorded
+	defer func() {
+		if err == nil && ctx.Err() == nil {
+			planned()
+		}
+	}()
 	// A template fixed to the target's origin makes the same requests for every
 	// target that shares one, which a crawled list produces by the hundred.
 	// Running it once per origin sends exactly the same traffic, minus the

pkg/core/plan.go

@@ -104,7 +104,7 @@ func planEntry(template *templates.Template, value *contextargs.MetaInput, selec
 	entry := PlanEntry{
 		Target:    value.Input,
 		IP:        value.CustomIP,
-		Templates: []string{template.ID},
+		Templates: planTemplates(template, selection),
 		Protocol:  template.Type().String(),
 		Requests:  template.TotalRequests,
 		Dynamic:   template.Flow != "" || template.IsFuzzableRequest(),
@@ -126,7 +126,6 @@ func planEntry(template *templates.Template, value *contextargs.MetaInput, selec
 		entry.Dynamic = true
 	case isCluster(template):
 		cluster := template.Executer.(*templates.ClusterExecuter)
-		entry.Templates = slices.Sorted(slices.Values(cluster.TemplateIDs(selection)))
 		// TotalRequests of a cluster counts only its http and dns requests,
 		// so an ssl cluster would show none
 		entry.Requests = cluster.Requests()
@@ -143,6 +142,15 @@ func planEntry(template *templates.Template, value *contextargs.MetaInput, selec
 	return entry
 }
 
+// planTemplates lists the templates an entry runs, sorted so the entry id does
+// not depend on clustering order.
+func planTemplates(template *templates.Template, selection protocols.TemplateSelection) []string {
+	if cluster, ok := template.Executer.(*templates.ClusterExecuter); ok {
+		return slices.Sorted(slices.Values(cluster.TemplateIDs(selection)))
+	}
+	return []string{template.ID}
+}
+
 func isCluster(template *templates.Template) bool {
 	_, ok := template.Executer.(*templates.ClusterExecuter)
 	return ok
@@ -154,3 +162,36 @@ func planEntryID(entry PlanEntry) string {
 	sum := sha256.Sum256([]byte(entry.Target + "\x00" + entry.IP + "\x00" + strings.Join(entry.Templates, "\x00")))
 	return hex.EncodeToString(sum[:8])
 }
+
+// PlanRun limits a scan to the entries of a plan and records the ones that
+// finish, so running the plan again resumes it.
+type PlanRun interface {
+	// Skip reports whether the entry is not in the plan or already finished.
+	Skip(id string) bool
+	// Finished records an entry that ran without error.
+	Finished(id string)
+}
+
+// SetPlanRun makes the scan run only the entries run allows.
+func (e *Engine) SetPlanRun(run PlanRun) {
+	e.planRun = run
+}
+
+// claimPlanned reports whether the pair is skipped under a plan run, and
+// otherwise returns the func that records it finished. Without a plan run
+// every pair runs.
+func (e *Engine) claimPlanned(template *templates.Template, value *contextargs.MetaInput) (finished func(), skip bool) {
+	if e.planRun == nil {
+		return func() {}, false
+	}
+	// as in Plan, a self-contained template is not narrowed by any target
+	var selection protocols.TemplateSelection
+	if !template.SelfContained {
+		selection = e.selectionFor(value)
+	}
+	id := planEntryID(PlanEntry{Target: value.Input, IP: value.CustomIP, Templates: planTemplates(template, selection)})
+	if e.planRun.Skip(id) {
+		return nil, true
+	}
+	return func() { e.planRun.Finished(id) }, false
+}

pkg/core/plan_test.go

@@ -154,3 +154,62 @@ func TestPlanListsOriginAlternatives(t *testing.T) {
 	})
 	require.Equal(t, plan, again)
 }
+
+// fixedPlanRun is a plan run over fixed ids that records the finished ones.
+type fixedPlanRun struct {
+	mu       sync.Mutex
+	allowed  map[string]bool
+	finished []string
+}
+
+func (a *fixedPlanRun) Skip(id string) bool { return !a.allowed[id] }
+
+func (a *fixedPlanRun) Finished(id string) {
+	a.mu.Lock()
+	defer a.mu.Unlock()
+	a.finished = append(a.finished, id)
+}
+
+func TestPlanRunRunsOnlyThePlannedPairs(t *testing.T) {
+	options := &types.Options{BulkSize: 2, TemplateThreads: 2, HeadlessBulkSize: 1, HeadlessTemplateThreads: 1}
+	engine := New(options)
+	engine.SetExecuterOptions(&protocols.ExecutorOptions{
+		Logger:       engine.Logger,
+		Options:      options,
+		ResumeCfg:    types.NewResumeCfg(),
+		ProtocolType: tmpltypes.HTTPProtocol,
+		Progress:     &progressRecorder{},
+		TargetScope:  scopeByInput{"php": {paths: []string{"thinkphp.yaml"}}},
+	})
+
+	var (
+		mu   sync.Mutex
+		runs []string
+	)
+	var templatesList []*templates.Template
+	for _, path := range []string{"thinkphp.yaml", "generic.yaml"} {
+		templatesList = append(templatesList, &templates.Template{
+			ID:            path,
+			Path:          path,
+			TotalRequests: 1,
+			Executer:      &recordingExecuter{path: path, mu: &mu, runs: &runs},
+		})
+	}
+	targets := &fakeTargetProvider{values: []*contextargs.MetaInput{{Input: "php"}, {Input: "plain"}}}
+
+	var plan []PlanEntry
+	engine.Plan(templatesList, targets, true, func(entry PlanEntry) { plan = append(plan, entry) })
+	require.Len(t, plan, 3)
+
+	// the first entry is left out of the plan, as if an agent removed it
+	run := &fixedPlanRun{allowed: map[string]bool{plan[1].ID: true, plan[2].ID: true}}
+	engine.SetPlanRun(run)
+	engine.ExecuteScanWithOpts(context.Background(), templatesList, targets, true)
+
+	var want []string
+	for _, entry := range plan[1:] {
+		want = append(want, entry.Templates[0]+"@"+entry.Target)
+	}
+	require.ElementsMatch(t, want, runs, "only the planned pairs run")
+	require.ElementsMatch(t, []string{plan[1].ID, plan[2].ID}, run.finished, "the scan derives the ids the plan wrote")
+}

pkg/reporting/trackers/jira/jira.go

@@ -7,7 +7,6 @@ import (
 	"net/http"
 	"net/url"
 	"strings"
-	"sync"
 	"text/template"
 
 	"github.com/andygrunwald/go-jira"
@@ -171,9 +170,6 @@ type Integration struct {
 	Formatter
 	jira    *jira.Client
 	options *Options
-
-	once         *sync.Once
-	transitionID string
 }
 
 // Options contains the configuration options for jira client
@@ -256,7 +252,6 @@ func New(options *Options) (*Integration, error) {
 	integration := &Integration{
 		jira:    jiraClient,
 		options: options,
-		once:    &sync.Once{},
 	}
 	return integration, nil
 }
@@ -404,40 +399,50 @@ func (i *Integration) CloseIssue(event *output.ResultEvent) error {
 		return nil
 	}
 
-	issue, err := i.FindExistingIssue(event, false)
+	issue, err := i.FindExistingIssue(event, true)
 	if err != nil {
 		return err
-	} else if issue.ID != "" {
-		// Lazy load the transitions ID in case it's not set.
-		// StatusNot is a target status name (matches JQL usage below and the
-		// field's semantics); find the transition that moves to that status.
-		i.once.Do(func() {
-			transitions, _, err := i.jira.Issue.GetTransitions(issue.ID)
-			if err != nil {
-				return
-			}
-			for _, transition := range transitions {
-				if transition.To.Name == i.options.StatusNot {
-					i.transitionID = transition.ID
-					break
-				}
-			}
-		})
-		if i.transitionID == "" {
-			return nil
-		}
-		transition := jira.CreateTransitionPayload{
-			Transition: jira.TransitionPayload{
-				ID: i.transitionID,
-			},
-		}
-
-		_, err = i.jira.Issue.DoTransitionWithPayload(issue.ID, transition)
-		if err != nil {
-			return err
-		}
 	}
-	return nil
+	if issue.ID == "" {
+		return nil
+	}
+	return i.CloseIssueByID(issue.ID)
+}
+
+// CloseIssueByID transitions a known Jira issue to the configured target status.
+func (i *Integration) CloseIssueByID(issueID string) error {
+	if i.options.StatusNot == "" {
+		return nil
+	}
+	if issueID == "" {
+		return fmt.Errorf("jira issue ID is required")
+	}
+
+	transitions, _, err := i.jira.Issue.GetTransitions(issueID)
+	if err != nil {
+		return fmt.Errorf("get Jira issue %s transitions: %w", issueID, err)
+	}
+	for _, transition := range transitions {
+		if transition.To.Name != i.options.StatusNot {
+			continue
+		}
+		_, err = i.jira.Issue.DoTransitionWithPayload(issueID, jira.CreateTransitionPayload{
+			Transition: jira.TransitionPayload{ID: transition.ID},
+		})
+		if err != nil {
+			return fmt.Errorf("transition Jira issue %s: %w", issueID, err)
+		}
+		return nil
+	}
+
+	currentIssue, _, err := i.jira.Issue.Get(issueID, nil)
+	if err != nil {
+		return fmt.Errorf("get Jira issue %s status: %w", issueID, err)
+	}
+	if currentIssue.Fields != nil && currentIssue.Fields.Status != nil && currentIssue.Fields.Status.Name == i.options.StatusNot {
+		return nil
+	}
+	return fmt.Errorf("jira issue %s has no transition to %q", issueID, i.options.StatusNot)
 }
 
 // FindExistingIssue checks if the issue already exists and returns its ID
@@ -495,12 +500,12 @@ func (i *Integration) FindExistingIssue(event *output.ResultEvent, useStatus boo
 		}, nil
 	}
 
-	searchOptions := &jira.SearchOptionsV2{
+	searchOptions := &jira.SearchOptions{
 		MaxResults: 1, // if any issue exists, then we won't create a new one
 		Fields:     []string{"summary", "description", "issuetype", "status", "priority", "project"},
 	}
 
-	issues, resp, err := i.jira.Issue.SearchV2JQL(jql, searchOptions)
+	issues, resp, err := i.jira.Issue.Search(jql, searchOptions)
 	if err != nil {
 		var data string
 		if resp != nil && resp.Body != nil {
@@ -510,7 +515,7 @@ func (i *Integration) FindExistingIssue(event *output.ResultEvent, useStatus boo
 		return jira.Issue{}, fmt.Errorf("%w => %s", err, data)
 	}
 
-	switch resp.Total {
+	switch len(issues) {
 	case 0:
 		return jira.Issue{}, nil
 	case 1:

pkg/reporting/trackers/jira/jira_test.go

@@ -1,7 +1,9 @@
 package jira
 
 import (
+	"fmt"
 	"net/http"
+	"net/http/httptest"
 	"os"
 	"strings"
 	"testing"
@@ -15,6 +17,188 @@ import (
 	"github.com/stretchr/testify/require"
 )
 
+func TestCloseIssueUsesServerSearchResult(t *testing.T) {
+	transitionCalls := 0
+	server := httptest.NewServer(http.HandlerFunc(func(w http.ResponseWriter, r *http.Request) {
+		switch {
+		case r.Method == http.MethodGet && strings.HasSuffix(r.URL.Path, "/search"):
+			_, _ = w.Write([]byte(`{"issues":[{"id":"10001","key":"TEST-1","fields":{"status":{"name":"Open"}}}]}`))
+		case r.Method == http.MethodGet && strings.HasSuffix(r.URL.Path, "/search/jql"):
+			http.Error(w, "", http.StatusForbidden)
+		case r.Method == http.MethodGet && strings.HasSuffix(r.URL.Path, "/transitions"):
+			_, _ = w.Write([]byte(`{"transitions":[{"id":"5","to":{"name":"Done"}}]}`))
+		case r.Method == http.MethodPost && strings.HasSuffix(r.URL.Path, "/transitions"):
+			transitionCalls++
+			w.WriteHeader(http.StatusNoContent)
+		default:
+			http.Error(w, "unexpected endpoint", http.StatusNotFound)
+		}
+	}))
+	defer server.Close()
+
+	integration, err := New(&Options{URL: server.URL, AccountID: "test", Token: "test", ProjectName: "TEST", StatusNot: "Done"})
+	require.NoError(t, err)
+	err = integration.CloseIssue(&output.ResultEvent{TemplateID: "pdcp-verify", Host: "example.test", Info: model.Info{Name: "Test issue"}})
+	require.NoError(t, err)
+	require.Equal(t, 1, transitionCalls)
+}
+
+func TestCloseIssueFindsOpenIssueWhenOlderMatchIsDone(t *testing.T) {
+	transitioned := ""
+	server := httptest.NewServer(http.HandlerFunc(func(w http.ResponseWriter, r *http.Request) {
+		switch {
+		case r.Method == http.MethodGet && strings.HasSuffix(r.URL.Path, "/search"):
+			if strings.Contains(r.URL.Query().Get("jql"), `status != "Done"`) {
+				_, _ = w.Write([]byte(`{"issues":[{"id":"10002","key":"TEST-2"}]}`))
+			} else {
+				_, _ = w.Write([]byte(`{"issues":[{"id":"10001","key":"TEST-1"}]}`))
+			}
+		case r.Method == http.MethodGet && strings.HasSuffix(r.URL.Path, "/issue/10001/transitions"):
+			_, _ = w.Write([]byte(`{"transitions":[]}`))
+		case r.Method == http.MethodGet && strings.HasSuffix(r.URL.Path, "/issue/10001"):
+			_, _ = w.Write([]byte(`{"fields":{"status":{"name":"Done"}}}`))
+		case r.Method == http.MethodGet && strings.HasSuffix(r.URL.Path, "/issue/10002/transitions"):
+			_, _ = w.Write([]byte(`{"transitions":[{"id":"5","to":{"name":"Done"}}]}`))
+		case r.Method == http.MethodPost && strings.HasSuffix(r.URL.Path, "/issue/10002/transitions"):
+			transitioned = "10002"
+			w.WriteHeader(http.StatusNoContent)
+		default:
+			http.Error(w, "unexpected endpoint", http.StatusNotFound)
+		}
+	}))
+	defer server.Close()
+
+	integration, err := New(&Options{URL: server.URL, AccountID: "test", Token: "test", ProjectName: "TEST", StatusNot: "Done"})
+	require.NoError(t, err)
+	err = integration.CloseIssue(&output.ResultEvent{TemplateID: "pdcp-verify", Host: "example.test", Info: model.Info{Name: "Test issue"}})
+	require.NoError(t, err)
+	require.Equal(t, "10002", transitioned)
+}
+
+func TestCloseIssueSearchesConfiguredProjectWhenEventHasAnotherJiraID(t *testing.T) {
+	searchCalls, transitionCalls := 0, 0
+	searchJQL := ""
+	server := httptest.NewServer(http.HandlerFunc(func(w http.ResponseWriter, r *http.Request) {
+		switch {
+		case r.Method == http.MethodGet && strings.HasSuffix(r.URL.Path, "/search"):
+			searchCalls++
+			searchJQL = r.URL.Query().Get("jql")
+			_, _ = w.Write([]byte(`{"issues":[{"id":"123","key":"TEST-1","fields":{"status":{"name":"Open"}}}]}`))
+		case r.Method == http.MethodGet && strings.HasSuffix(r.URL.Path, "/search/jql"):
+			http.Error(w, "", http.StatusForbidden)
+		case r.Method == http.MethodGet && strings.HasSuffix(r.URL.Path, "/issue/123/transitions"):
+			_, _ = w.Write([]byte(`{"transitions":[{"id":"5","to":{"name":"Done"}}]}`))
+		case r.Method == http.MethodPost && strings.HasSuffix(r.URL.Path, "/issue/123/transitions"):
+			transitionCalls++
+			w.WriteHeader(http.StatusNoContent)
+		default:
+			http.Error(w, "unexpected endpoint", http.StatusNotFound)
+		}
+	}))
+	defer server.Close()
+
+	integration, err := New(&Options{URL: server.URL, AccountID: "test", Token: "test", ProjectName: "TEST", StatusNot: "Done"})
+	require.NoError(t, err)
+	err = integration.CloseIssue(&output.ResultEvent{
+		TemplateID: "pdcp-verify",
+		Host:       "example.test",
+		IssueTrackers: map[string]output.IssueTrackerMetadata{
+			"jira": {IssueID: "10001", IssueURL: server.URL + "/browse/OTHER-1"},
+		},
+	})
+	require.NoError(t, err)
+	require.Equal(t, 1, searchCalls)
+	require.Contains(t, searchJQL, `project = "TEST"`)
+	require.Equal(t, 1, transitionCalls)
+}
+
+func TestCloseIssueByIDTargetsOnlyCreatedTicket(t *testing.T) {
+	searchCalls, transitionCalls := 0, 0
+	server := httptest.NewServer(http.HandlerFunc(func(w http.ResponseWriter, r *http.Request) {
+		switch {
+		case r.Method == http.MethodGet && strings.Contains(r.URL.Path, "/search"):
+			searchCalls++
+			http.Error(w, "", http.StatusForbidden)
+		case r.Method == http.MethodGet && strings.HasSuffix(r.URL.Path, "/issue/10001/transitions"):
+			_, _ = w.Write([]byte(`{"transitions":[{"id":"5","to":{"name":"Done"}}]}`))
+		case r.Method == http.MethodPost && strings.HasSuffix(r.URL.Path, "/issue/10001/transitions"):
+			transitionCalls++
+			w.WriteHeader(http.StatusNoContent)
+		default:
+			http.Error(w, "unexpected endpoint", http.StatusNotFound)
+		}
+	}))
+	defer server.Close()
+
+	integration, err := New(&Options{URL: server.URL, AccountID: "test", Token: "test", ProjectName: "TEST", StatusNot: "Done"})
+	require.NoError(t, err)
+	err = integration.CloseIssueByID("10001")
+	require.NoError(t, err)
+	require.Zero(t, searchCalls)
+	require.Equal(t, 1, transitionCalls)
+}
+
+func TestCloseIssueReportsTransitionLookupFailure(t *testing.T) {
+	transitionLookups := 0
+	server := httptest.NewServer(http.HandlerFunc(func(w http.ResponseWriter, r *http.Request) {
+		switch {
+		case r.Method == http.MethodGet && strings.HasSuffix(r.URL.Path, "/search"):
+			_, _ = w.Write([]byte(`{"issues":[{"id":"10001","key":"TEST-1","fields":{"status":{"name":"Open"}}}]}`))
+		case r.Method == http.MethodGet && strings.HasSuffix(r.URL.Path, "/search/jql"):
+			http.Error(w, "", http.StatusForbidden)
+		case r.Method == http.MethodGet && strings.HasSuffix(r.URL.Path, "/transitions"):
+			transitionLookups++
+			http.Error(w, "", http.StatusForbidden)
+		default:
+			http.Error(w, "unexpected endpoint", http.StatusNotFound)
+		}
+	}))
+	defer server.Close()
+
+	integration, err := New(&Options{URL: server.URL, AccountID: "test", Token: "test", ProjectName: "TEST", StatusNot: "Done"})
+	require.NoError(t, err)
+	err = integration.CloseIssue(&output.ResultEvent{TemplateID: "pdcp-verify", Host: "example.test", Info: model.Info{Name: "Test issue"}})
+	require.ErrorContains(t, err, fmt.Sprint(http.StatusForbidden))
+	require.Equal(t, 1, transitionLookups)
+}
+
+func TestCloseIssueWithoutTargetTransition(t *testing.T) {
+	for _, tc := range []struct {
+		status  string
+		wantErr bool
+	}{
+		{status: "Open", wantErr: true},
+		{status: "Done", wantErr: false},
+	} {
+		t.Run(tc.status, func(t *testing.T) {
+			server := httptest.NewServer(http.HandlerFunc(func(w http.ResponseWriter, r *http.Request) {
+				switch {
+				case r.Method == http.MethodGet && strings.HasSuffix(r.URL.Path, "/search"):
+					_, _ = w.Write([]byte(`{"issues":[{"id":"10001","key":"TEST-1","fields":{"status":{"name":"Open"}}}]}`))
+				case r.Method == http.MethodGet && strings.HasSuffix(r.URL.Path, "/transitions"):
+					_, _ = w.Write([]byte(`{"transitions":[]}`))
+				case r.Method == http.MethodGet && strings.HasSuffix(r.URL.Path, "/issue/10001"):
+					_, _ = fmt.Fprintf(w, `{"fields":{"status":{"name":%q}}}`, tc.status)
+				default:
+					http.Error(w, "unexpected endpoint", http.StatusNotFound)
+				}
+			}))
+			defer server.Close()
+
+			integration, err := New(&Options{URL: server.URL, AccountID: "test", Token: "test", StatusNot: "Done"})
+			require.NoError(t, err)
+			err = integration.CloseIssue(&output.ResultEvent{IssueTrackers: map[string]output.IssueTrackerMetadata{
+				"jira": {IssueID: "10001"},
+			}})
+			if tc.wantErr {
+				require.ErrorContains(t, err, "no transition")
+			} else {
+				require.NoError(t, err)
+			}
+		})
+	}
+}
+
 type recordingTransport struct {
 	inner http.RoundTripper
 	paths []string

pkg/types/types.go

@@ -254,6 +254,9 @@ type Options struct {
 	// PlanFile is where the work a scan would do is written as JSON lines;
 	// nuclei exits after writing it, without sending requests.
 	PlanFile string
+	// RunPlanFile is a plan whose entries the scan runs, skipping those its
+	// done log lists as finished.
+	RunPlanFile string
 	// StoreEvents is where the scan writes the event of every request, as
 	// JSON lines, for -replay.
 	StoreEvents string
@@ -721,6 +724,7 @@ func (options *Options) Copy() *Options {
 		Silent:                         options.Silent,
 		Validate:                       options.Validate,
 		PlanFile:                       options.PlanFile,
+		RunPlanFile:                    options.RunPlanFile,
 		StoreEvents:                    options.StoreEvents,
 		ReplayFile:                     options.ReplayFile,
 		NoStrictSyntax:                 options.NoStrictSyntax,

pkg/types/types_test.go

@@ -18,10 +18,13 @@ func TestCopyPreservesPayloadRandomOrder(t *testing.T) {
 }
 
 func TestCopyPreservesPlanFile(t *testing.T) {
-	options := &Options{PlanFile: "plan.jsonl"}
+	options := &Options{PlanFile: "plan.jsonl", RunPlanFile: "run.jsonl"}
 	if options.Copy().PlanFile != "plan.jsonl" {
 		t.Fatal("Copy must preserve PlanFile, or an embedded caller loses plan mode")
 	}
+	if options.Copy().RunPlanFile != "run.jsonl" {
+		t.Fatal("Copy must preserve RunPlanFile, or an embedded caller runs the whole scan")
+	}
 }
 
 func TestToJSONMapRejectsKeysSharingAStringForm(t *testing.T) {