A Study of Treatment of Inflammation Before Stem Cell Transplant in People With a Primary Immune Regulatory Disorder (PIRD) and/or an Autoinflammatory Condition

Inclusion Criteria: * Patients receiving first allo-HCT for the following immunologic conditions: * Primary Immune Regulatory Disorder with or without a genetic lesion as defined by the Primary Immune Deficiency Treatment Consortium (PIDTC) * Patients with autoinflammatory disorders evidenced by cytokine or inflammation assays with at least 1.5x ULN of measured cytokines and/or an elevated ferritin or ESR \> 2 ULN * For inclusion on the emapalumab group, the lesion must be isolated to the IFNγ pathway (or mediators thereof) with an elevated CXCL9 \>1.5 ULN OR sIL2R \>1.5 ULN (or already controlled on immune modulation, provided that CXCL9 or sIL2R levels were elevated prior to initiation of immune modulation). Inclusion on the Fludarabine/dexamethasone group requires inflammation (as defined above) other than an isolated IFNγ pathway * Able to tolerate cytoreduction (based on adequate organ function as described below) * Patients of any age can enroll so long as they meet other inclusion criteria: * Adequate organ function is required, defined as follows: * Hepatic: Serum bilirubin ≤ 2 mg/dL, unless benign congenital hyperbilirubinemia. Patients with hyperbilirubinemia related to paroxysmal nocturnal hemoglobinuria or other hemolytic disorders related to their PIRD diagnosis are eligible. * Hepatic: AST, ALT, and alkaline phosphatase \< 2.5 times the upper limit of normal unless thought to be disease-related. Investigator will need to perform clinically indicated evaluations to assess if disease related or intrinsic liver disease. Additional testing may be done if clinically indicated, after the pre-transplant immune prophase and prior to start of conditioning as this will provide additional data to confirm disease related versus intrinsic liver dysfunction. * Renal: serum creatinine \<1.5x normal for age. If serum creatinine is outside the normal range, then CrCl \> 50 mL/min/1.73m2 (calculated or estimated) or GFR (mL/min/1.72m2) \>30% of predicted normal for age. * Normal GFR by Age * Cardiac: LVEF ≥ 50% by MUGA or resting echocardiogram. * Pulmonary: Pulmonary function testing (FEV1 and corrected DLCO) ≥ 50% predicted (pediatric patients unable to complete PFTs will need oxygen saturation as recorded by pulse oximetry of ≥92% on room air). * Adequate performance status: * Age ≥ 16 years: ECOG ≤ 1 or Karnofsky 70% * Age \< 16 years: Lansky 70% * Each patient must be willing to participate as a research subject and must sign an informed consent form or legal guardian with assent as appropriate. Exclusion Criteria: * Uncontrolled infection at the time of enrollment. * Patients who have undergone previous allo-HCT. * Patient seropositivity for HIV I/II and/or HTLV I/II. * Females who are pregnant or breastfeeding. * Patients unwilling to use contraception during the study period. * Patient or parent or guardian unable to give informed consent or unable to comply with the treatment protocol including research tests. Donor Inclusion Criteria: * Related Donors: * 8/8 or 7/8 HLA matched at A, B, C, and DRB1 loci, as tested by DNA analysis. * Haploidentical donors at A, B, C and DRB1 loci, as tested by DNA analysis * Unrelated Donors: o 8/8 or 7/8 matched at A, B, C, and DRB1 loci, as tested by DNA analysis. * Able to provide informed consent for the donation process per institutional standards. * Meet standard criteria for donor collection (e.g. National Marrow Donor Program Guidelines or collecting center guidelines as approved by treating physician).