shell: kill process group on timeout/cancel (no orphans) + shell_bg job registry + kill_job/list_jobs

Root cause of the shell->shell_bg thrash: run() backgrounded POSIX commands
with a bare & and never captured the pid, so on timeout it returned an error
while the children kept running. Now: setsid (own process group), capture the
leader pid, SIGTERM+SIGKILL the whole group on timeout/cancel, and a message
telling the model it was killed + to use shell_bg. Plus shell_bg registers jobs
to /tmp/lmcp-bg-jobs.tsv and new kill_job/list_jobs let a runaway job be reaped
without a reboot.

server.lua

@@ -174,22 +174,39 @@ local function run(cmd, timeout_sec)
         end
         return output and output ~= "" and output or "(no output)"
     else
-        -- POSIX: use shell backgrounding + wait with timeout
-        -- sh -c '(cmd > out 2>&1; echo $? > done) &' then poll
+        -- POSIX: run in its OWN session/process group (setsid) so a
+        -- timeout or cancel can kill the WHOLE tree instead of orphaning
+        -- backgrounded children (the classic "shell timed out, children
+        -- kept thrashing" bug). $! is the setsid leader pid == pgid.
+        local pid_file = base .. ".pid"
         local sh_cmd = string.format(
             "(%s) > '%s' 2>&1; echo $? > '%s'",
             cmd, out_file, done_file
         )
-        os.execute("sh -c '" .. sh_cmd:gsub("'", "'\\''") .. "' &")
+        os.execute("setsid sh -c '" .. sh_cmd:gsub("'", "'\\''")
+            .. "' & echo $! > '" .. pid_file .. "'")
+        local pgid = (read_file(pid_file) or ""):match("(%d+)")
+        remove_silent(pid_file)
 
         local completed = poll_loop()
+
+        -- Timeout or cancel -> kill the entire process group. No orphans.
+        if not completed and pgid then
+            os.execute("kill -TERM -" .. pgid .. " 2>/dev/null")
+            sleep_ms(300)
+            os.execute("kill -KILL -" .. pgid .. " 2>/dev/null")
+        end
+
         local output = read_file(out_file)
         remove_silent(out_file)
         remove_silent(done_file)
 
         if not completed then
-            if cancelled then return "(cancelled)" end
-            return output or ("Error: command timed out after " .. timeout_sec .. "s")
+            if cancelled then return "(cancelled -- process group killed)" end
+            return (output and output ~= "" and (output .. "\n") or "")
+                .. "Error: command timed out after " .. timeout_sec
+                .. "s -- the process group was KILLED (nothing is still running). "
+                .. "For a long-running command, re-run it with shell_bg."
         end
         return output and output ~= "" and output or "(no output)"
     end
@@ -283,7 +300,15 @@ server:tool("shell_bg",
             f:close()
             os.remove(pid_file)
         end
-        return string.format("launched pid=%s log=%s", pid, log)
+        -- register so list_jobs/kill_job can see and reap it (no more reboots)
+        if pid ~= "?" then
+            local reg = io.open("/tmp/lmcp-bg-jobs.tsv", "a")
+            if reg then
+                reg:write(pid.."\t"..log.."\t"..os.date("%Y-%m-%dT%H:%M:%S").."\t"..inner:gsub("[\t\n]"," ").."\n")
+                reg:close()
+            end
+        end
+        return string.format("launched pid=%s log=%s (kill with kill_job pid=%s)", pid, log, pid)
     end, {
         annotations = {
             title           = "Run shell (background)",
@@ -294,6 +319,42 @@ server:tool("shell_bg",
         },
     })
 
+server:tool("kill_job",
+    "Kill a runaway background job by PID. SIGKILLs the whole process group of a shell_bg/setsid job so no children survive. Use when a background job is thrashing a machine.",
+    { type = "object", properties = { pid = { type = "integer", description = "PID from shell_bg / list_jobs" } }, required = { "pid" } },
+    function(a)
+        if WINDOWS then return "Error: kill_job is Linux-only" end
+        local pid = tostring(a.pid or ""):match("(%d+)")
+        if not pid then return "Error: numeric pid required" end
+        os.execute("kill -KILL -"..pid.." 2>/dev/null; kill -KILL "..pid.." 2>/dev/null")
+        sleep_ms(200)
+        local alive = os.execute("kill -0 "..pid.." 2>/dev/null")
+        if alive == true or alive == 0 then return "pid "..pid.." may still be alive (uninterruptible?)" end
+        return "killed pid "..pid.." (process group)"
+    end,
+    { annotations = { title = "Kill background job", destructiveHint = true } })
+
+server:tool("list_jobs",
+    "List background jobs started via shell_bg and whether each is still running. Use to find runaway jobs to kill_job.",
+    { type = "object", properties = {} },
+    function()
+        if WINDOWS then return "Error: list_jobs is Linux-only" end
+        local reg = io.open("/tmp/lmcp-bg-jobs.tsv", "r")
+        if not reg then return "(no background jobs recorded)" end
+        local out = {}
+        for line in reg:lines() do
+            local pid, log, ts, cmd = line:match("^(%d+)\t([^\t]*)\t([^\t]*)\t(.*)$")
+            if pid then
+                local alive = os.execute("kill -0 "..pid.." 2>/dev/null")
+                local st = (alive == true or alive == 0) and "RUNNING" or "done"
+                table.insert(out, string.format("pid=%s [%s] %s log=%s\n    %s", pid, st, ts, log, (cmd or ""):sub(1,100)))
+            end
+        end
+        reg:close()
+        return #out>0 and table.concat(out, "\n") or "(no background jobs recorded)"
+    end,
+    { annotations = { title = "List background jobs", readOnlyHint = true } })
+
 server:tool("read_file", "Read a file.", {
     type = "object",
     properties = { path = { type = "string" } },