Patients must have evidence of acute leukemia in their peripheral blood or bone marrow; patients must have >= % blasts in the peripheral blood or bone marrow within days prior to registration; at least >= % of those blasts must be CD-positive (surface) based on local immunophenotyping and histopathology Presence of circulating leukemic blasts (in the peripheral blood) detected by standard pathology for patients with AML, ALL or CML Presence of >= % circulating leukemic blasts (in the peripheral blood) detected by standard pathology for patients with MDS/MPS Hyperleukocytosis with ? , leukemic blasts/L blood (hydroxyurea permitted up to hours prior to beginning study drugs) High-risk MDS/CMML (defined as ? % peripheral blood or marrow blasts and/or IPSS score ? .) and relapsed or refractory to prior therapy Fewer than % blasts in the bone marrow or peripheral blood Had accelerated phase or leukemic transformation (>= % blasts in peripheral blood [PB] or bone marrow [BM] any time prior to HCT) Peripheral blood blasts ? % Prior chemotherapy for AML. Hydroxyurea is allowed for the control of peripheral leukemic blasts in subjects with leukocytosis Presence of circulating blasts (in the blood) detected by standard pathology for patients with AML, ALL or CML Presence of >= % circulating leukemic blasts (in the blood) detected by standard pathology for patients with MDS/MPS/CMML No blasts or promyelocytes in peripheral blood Patients with AML must have less than % bone marrow blasts and < /mcL absolute peripheral blood blast count For subjects with ALL or AML, presence of >% blasts in the bone marrow (based on a bone marrow aspirate/biopsy sample with ? nucleated cells and the presence of bone marrow spicules) and/or > x /L blasts in the peripheral blood (with the restriction that peripheral blast count in subjects with AML must be < x /L prior to the start of study therapy). Blasts in Peripheral Blood or Bone Marrow ?% (either myeloid or lymphoid blasts) Promyelocytes and Blasts in Peripheral Blood or Bone Marrow ?% Cytogenetic clonal evolution Blast phase is defined as ?% blasts in peripheral blood or bone marrow, or presence of extramedullary disease, except for liver or spleen. Relapsed ALL defined as > % malignant blasts in bone marrow or peripheral blood Either bone marrow or peripheral blood is allowed For cohort only: patients with a bone marrow biopsy with < % cellularity, evidence of collagen fibrosis, osteosclerosis, or blasts > % in peripheral blood or marrow (demonstrating advanced disease) RECIPIENT: Patients may have evidence of MDS with one or more peripheral blood cytopenias and greater than % blasts but less than % blasts in the bone marrow in the absence of filgrastim Patients with CML-AP or CML-BP or Philadelphia chromosome-positive acute myeloid leukemia defined as follows: CML-AP is defined by the presence of -% blasts in peripheral blood (PB) or bone marrow (BM), >= % basophils in PB or BM, >= % blasts plus promyelocytes (with blasts < %) in PB or BM, < x ^/L platelets unrelated to therapy, or by clonal cytogenetics evolution (i.e., the presence of cytogenetic abnormalities other than the Philadelphia chromosome); CML-BP is defined by the presence of >= % blasts in the bone marrow and/or peripheral blood or the presence of extramedullary disease Aspartate aminotransferase (AST) =< x the institutional ULN, measured prior to conditioning chemotherapy; elevation secondary to leukemic involvement is not an exclusion criterion; leukemic involvement will be determined by the presence of progressive relapse defined by escalating bone marrow or peripheral blood leukemia blasts within the previous month and the absence of initiation of known hepatotoxic medication (e.g. azoles) Greater than % blasts in bone marrow or greater than % in peripheral blood <% peripheral blood blasts. Acute myeloid leukemia-intermediate risk as defined by standard World Health Organization (WHO) criteria for AML (at least % blasts in the peripheral blood or bone marrow) at the time of initial diagnosis\r\n* Diagnosis of AML according to WHO diagnostic criteria (at least % blasts in the peripheral blood or bone marrow), with FrenchAmericanBritish (FAB) classification other than M (acute promyelocytic leukemia), documented by bone marrow aspiration and biopsy performed within days prior to administration of st dose of remission induction chemotherapy Have previously untreated AML, defined according to WHO criteria, with ? % leukemic blasts in the bone marrow. Subjects with extramedullary disease alone (ie, no detectable bone marrow and no detectable peripheral blood AML) are not eligible for the study. Subjects who have been diagnosed as having AML with peripheral blood or bone marrow blasts of ?%. Cytogenetic analysis must be performed from diagnostic bone marrow (preferred) or if adequate number of circulating blasts (> ^/l) from peripheral blood Blasts in the peripheral blood (PB) and bone marrow (BM) < % prior to study enrollment Leukemic transformation (> % blasts in peripheral blood or bone marrow biopsy). Relapsed or refractory AML patients with at least % blasts by bone marrow biopsy or aspirate, or at least % blasts in peripheral blood, not likely to benefit from standard salvage chemotherapy. Presence of >= % circulating leukemic blasts (in the peripheral blood) detected by standard pathology Aspartate aminotransferase (AST) =< x the institutional ULN; elevation secondary to leukemic involvement is not an exclusion criterion; leukemic involvement will be determined by the presence of progressive relapsed defined by escalating bone marrow or peripheral blood leukemia blasts within the previous month and the absence of initiation of known hepatotoxic medication (e.g. azoles) Presence of circulating leukemic blasts in the peripheral blood detected by standard morphology Chronic phase disease is defined as:\r\n* < % blasts in peripheral blood and bone marrow; \r\n* < % blasts plus promyelocytes in peripheral blood and bone marrow;\r\n* < % basophils in peripheral blood; \r\n* >= x ^/L platelets (>= ,/mm^); \r\n* No evidence of extramedullary disease except hepatosplenomegaly; and \r\n* No prior diagnosis of accelerated phase (AP) or blastic phase-chronic myeloid leukemia (BP-CML); patients with clonal evolution but no other criteria for accelerated phase are eligible Blast phase disease (> % blasts in the marrow or peripheral blood) Documented excessive leukemic myeloid blasts in the bone marrow or peripheral blood (>= %) in the past months Pathological diagnosis of AML according to WHO criteria (with at least % blasts in the peripheral blood or bone marrow) Presence of circulating leukemic blasts (in the peripheral blood) detected by standard pathology for patients with AML, ALL or CML Presence of >= % circulating leukemic blasts (in the peripheral blood) detected by standard pathology for patients with MDS/MPS Blasts in Peripheral Blood or Bone Marrow ?% Promyelocytes and Blasts in Peripheral Blood or Bone Marrow ?% Thrombocytopenia < x /ml, not resulting from therapy Blast phase is defined as ?% blasts in peripheral blood or bone marrow, or presence of extramedullary disease, except for liver or spleen. Patients with AML, MDS, ALL, or CML must not have presence of circulating leukemic blasts detected by standard pathology Remission will be defined as < % blasts in the peripheral blood and bone marrow without morphological characteristics of the original leukemia population at the time of diagnosis Patients must have a strong clinical suspicion of JMML, based on a modified category of the revised diagnostic criteria; specifically, eligible patients must have all of the following: \r\n* Splenomegaly\r\n* Absolute monocyte count (AMC) > /uL\r\n* Blasts in peripheral blood (PB)/bone marrow (BM) < % Blast phase disease (>% blasts in the marrow or peripheral blood) Patients with AML must have less than % bone marrow blasts and no peripheral blood blasts EXCLUSION CRITERIA FOR ENROLLMENT (PRE-TRANSPLANT): Active leukemia (> % leukemic blasts in peripheral blood or bone marrow) EXCLUSION CRITERIA (PRIOR TO IBRUTINIB ADMINISTRATION): Relapsed leukemia (> % leukemic blasts in peripheral blood or bone marrow after allogeneic HCT) MDS\r\n* Bone marrow with =< percent myeloblasts with normal maturation of all cell lines\r\n* Peripheral blood demonstrates hemoglobin >= g/dL, platelets >= x ^/L, neutrophils >= x ^/L, and no circulating blasts The patient has a confirmed diagnosis of Philadelphia chromosome (Ph) positive chronic myelogenous leukemia in either CP or AP. Accelerated phase will be defined as disease having of the following: ?% to <% blasts in peripheral blood or bone marrow; ?% blasts + promyelocytes in peripheral blood or bone marrow; ?% basophils in peripheral blood or bone marrow; platelet count